# Minimization in vacuum without PBC

**URL:** <https://gromacs.bioexcel.eu/t/minimization-in-vacuum-without-pbc/110>\
**Category:** User discussions\
**Tags:** energy-minization\
**Created:** [May 11, 2020, 3:23pm UTC](https://gromacs.bioexcel.eu/t/minimization-in-vacuum-without-pbc/110 "2020-05-11T15:23:39Z")\
**Posts on this page:** 15\
**Page:** 1

<div class="post-metadata">

**Author:** ![ericpellegrini](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ericpellegrini/32/43_2.png) [@ericpellegrini](https://gromacs.bioexcel.eu/u/ericpellegrini)\
**Post date:** [May 11, 2020, 3:23pm UTC](https://gromacs.bioexcel.eu/t/minimization-in-vacuum-without-pbc/110/1 "2020-05-11T15:23:40Z")

</div>

GROMACS version: 2020  
GROMACS modification: No

I am a newbie with Gromacs and following an example script found in [this tutorial](http://cgmartini.nl/~mdcourse/pepmd/md.html) I fail to reproduce the minimization step in vacuum without PBC. The failure coming from the fact that the script is deprecated when used with gromacs 2020. Here is the contents of the script:

> ;  
> ; File ‘mdout.mdp’ was generated  
> ; By user: alex (22065)  
> ; On host: md02  
> ; At date: Thu Mar 23 09:13:15 2017
> 
> ;  
> ; Created by:  
> ; :-) GROMACS - gmx grompp, 2016.1 (-:  
> ;   
> ; Executable: /usr/local/gromacs-2016.1/bin/gmx  
> ; Data prefix: /usr/local/gromacs-2016.1  
> ; Working dir: /coarse/alex/TUTORIALS/pepmd-v5/md-tutorial  
> ; Command line:  
> ; gmx grompp -p protein.top -c protein.gro -f minim.mdp -o protein-EM-vacuum.tpr
> 
> ; VARIOUS PREPROCESSING OPTIONS  
> ; Preprocessor information: use cpp syntax.  
> ; e.g.: -I/home/joe/doe -I/home/mary/roe  
> include =  
> ; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)  
> define = -DFLEXIBLE
> 
> ; RUN CONTROL PARAMETERS  
> integrator = steep  
> ; Start time and timestep in ps  
> tinit = 0  
> dt = 0.001  
> nsteps = 500  
> ; For exact run continuation or redoing part of a run  
> init-step = 0  
> ; Part index is updated automatically on checkpointing (keeps files separate)  
> simulation-part = 1  
> ; mode for center of mass motion removal  
> comm-mode = Linear  
> ; number of steps for center of mass motion removal  
> nstcomm = 100  
> ; group(s) for center of mass motion removal  
> comm-grps =
> 
> ; LANGEVIN DYNAMICS OPTIONS  
> ; Friction coefficient (amu/ps) and random seed  
> bd-fric = 0  
> ld-seed = -1
> 
> ; ENERGY MINIMIZATION OPTIONS  
> ; Force tolerance and initial step-size  
> emtol = 1.0  
> emstep = 0.01  
> ; Max number of iterations in relax-shells  
> niter = 20  
> ; Step size (ps^2) for minimization of flexible constraints  
> fcstep = 0  
> ; Frequency of steepest descents steps when doing CG  
> nstcgsteep = 1000  
> nbfgscorr = 10
> 
> ; TEST PARTICLE INSERTION OPTIONS  
> rtpi = 0.05
> 
> ; OUTPUT CONTROL OPTIONS  
> ; Output frequency for coords (x), velocities (v) and forces (f)  
> nstxout = 0  
> nstvout = 0  
> nstfout = 0  
> ; Output frequency for energies to log file and energy file  
> nstlog = 1000  
> nstcalcenergy = 100  
> nstenergy = 1  
> ; Output frequency and precision for .xtc file  
> nstxout-compressed = 0  
> compressed-x-precision = 1000  
> ; This selects the subset of atoms for the compressed  
> ; trajectory file. You can select multiple groups. By  
> ; default, all atoms will be written.  
> compressed-x-grps =  
> ; Selection of energy groups  
> energygrps = System
> 
> ; NEIGHBORSEARCHING PARAMETERS  
> ; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)  
> cutoff-scheme = Group  
> ; nblist update frequency  
> nstlist = 10  
> ; ns algorithm (simple or grid)  
> ns\_type = simple  
> ; Periodic boundary conditions: xyz, no, xy  
> pbc = no  
> periodic-molecules = no  
> ; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,  
> ; a value of -1 means: use rlist  
> verlet-buffer-tolerance = 0.005  
> ; nblist cut-off  
> rlist = 1  
> ; long-range cut-off for switched potentials
> 
> ; OPTIONS FOR ELECTROSTATICS AND VDW  
> ; Method for doing electrostatics  
> coulombtype = cut-off  
> coulomb-modifier = Potential-shift-Verlet  
> rcoulomb-switch = 0  
> rcoulomb = 1.0  
> ; Relative dielectric constant for the medium and the reaction field  
> epsilon-r = 1  
> epsilon-rf = 0  
> ; Method for doing Van der Waals  
> vdw-type = Cut-off  
> vdw-modifier = Potential-shift-Verlet  
> ; cut-off lengths  
> rvdw-switch = 0  
> rvdw = 1.0  
> ; Apply long range dispersion corrections for Energy and Pressure  
> DispCorr = No  
> ; Extension of the potential lookup tables beyond the cut-off  
> table-extension = 1  
> ; Separate tables between energy group pairs  
> energygrp-table =  
> ; Spacing for the PME/PPPM FFT grid  
> fourierspacing = 0.12  
> ; FFT grid size, when a value is 0 fourierspacing will be used  
> fourier-nx = 0  
> fourier-ny = 0  
> fourier-nz = 0  
> ; EWALD/PME/PPPM parameters  
> pme-order = 4  
> ewald-rtol = 1e-05  
> ewald-rtol-lj = 0.001  
> lj-pme-comb-rule = Geometric  
> ewald-geometry = 3d  
> epsilon-surface = 0
> 
> ; IMPLICIT SOLVENT ALGORITHM  
> implicit-solvent = No
> 
> ; GENERALIZED BORN ELECTROSTATICS  
> ; Algorithm for calculating Born radii  
> gb-algorithm = Still  
> ; Frequency of calculating the Born radii inside rlist  
> nstgbradii = 1  
> ; Cutoff for Born radii calculation; the contribution from atoms  
> ; between rlist and rgbradii is updated every nstlist steps  
> rgbradii = 1  
> ; Dielectric coefficient of the implicit solvent  
> gb-epsilon-solvent = 80  
> ; Salt concentration in M for Generalized Born models  
> gb-saltconc = 0  
> ; Scaling factors used in the OBC GB model. Default values are OBC(II)  
> gb-obc-alpha = 1  
> gb-obc-beta = 0.8  
> gb-obc-gamma = 4.85  
> gb-dielectric-offset = 0.009  
> sa-algorithm = Ace-approximation  
> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA  
> ; The value -1 will set default value for Still/HCT/OBC GB-models.  
> sa-surface-tension = -1
> 
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS  
> ; Temperature coupling  
> tcoupl = No  
> nsttcouple = -1  
> nh-chain-length = 10  
> print-nose-hoover-chain-variables = no  
> ; Groups to couple separately  
> tc-grps =  
> ; Time constant (ps) and reference temperature (K)  
> tau-t =  
> ref-t =  
> ; pressure coupling  
> pcoupl = No  
> pcoupltype = Isotropic  
> nstpcouple = -1  
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)  
> tau-p = 1  
> compressibility =  
> ref-p =  
> ; Scaling of reference coordinates, No, All or COM  
> refcoord-scaling = No
> 
> ; OPTIONS FOR QMMM calculations  
> QMMM = no  
> ; Groups treated Quantum Mechanically  
> QMMM-grps =  
> ; QM method  
> QMmethod =  
> ; QMMM scheme  
> QMMMscheme = normal  
> ; QM basisset  
> QMbasis =  
> ; QM charge  
> QMcharge =  
> ; QM multiplicity  
> QMmult =  
> ; Surface Hopping  
> SH =  
> ; CAS space options  
> CASorbitals =  
> CASelectrons =  
> SAon =  
> SAoff =  
> SAsteps =  
> ; Scale factor for MM charges  
> MMChargeScaleFactor = 1  
> ; Optimization of QM subsystem  
> bOPT =  
> bTS =
> 
> ; SIMULATED ANNEALING  
> ; Type of annealing for each temperature group (no/single/periodic)  
> annealing =  
> ; Number of time points to use for specifying annealing in each group  
> annealing-npoints =  
> ; List of times at the annealing points for each group  
> annealing-time =  
> ; Temp. at each annealing point, for each group.  
> annealing-temp =
> 
> ; GENERATE VELOCITIES FOR STARTUP RUN  
> gen-vel = no  
> gen-temp = 300  
> gen-seed = -1
> 
> ; OPTIONS FOR BONDS  
> constraints = none  
> ; Type of constraint algorithm  
> constraint-algorithm = Lincs  
> ; Do not constrain the start configuration  
> continuation = no  
> ; Use successive overrelaxation to reduce the number of shake iterations  
> Shake-SOR = no  
> ; Relative tolerance of shake  
> shake-tol = 0.0001  
> ; Highest order in the expansion of the constraint coupling matrix  
> lincs-order = 4  
> ; Number of iterations in the final step of LINCS. 1 is fine for  
> ; normal simulations, but use 2 to conserve energy in NVE runs.  
> ; For energy minimization with constraints it should be 4 to 8.  
> lincs-iter = 1  
> ; Lincs will write a warning to the stderr if in one step a bond  
> ; rotates over more degrees than  
> lincs-warnangle = 30  
> ; Convert harmonic bonds to morse potentials  
> morse = no
> 
> ; ENERGY GROUP EXCLUSIONS  
> ; Pairs of energy groups for which all non-bonded interactions are excluded  
> energygrp-excl =
> 
> ; WALLS  
> ; Number of walls, type, atom types, densities and box-z scale factor for Ewald  
> nwall = 0  
> wall-type = 9-3  
> wall-r-linpot = -1  
> wall-atomtype =  
> wall-density =  
> wall-ewald-zfac = 3
> 
> ; COM PULLING  
> pull = no
> 
> ; ENFORCED ROTATION  
> ; Enforced rotation: No or Yes  
> rotation = no
> 
> ; Group to display and/or manipulate in interactive MD session  
> IMD-group =
> 
> ; NMR refinement stuff  
> ; Distance restraints type: No, Simple or Ensemble  
> disre = No  
> ; Force weighting of pairs in one distance restraint: Conservative or Equal  
> disre-weighting = Conservative  
> ; Use sqrt of the time averaged times the instantaneous violation  
> disre-mixed = no  
> disre-fc = 1000  
> disre-tau = 0  
> ; Output frequency for pair distances to energy file  
> nstdisreout = 100  
> ; Orientation restraints: No or Yes  
> orire = no  
> ; Orientation restraints force constant and tau for time averaging  
> orire-fc = 0  
> orire-tau = 0  
> orire-fitgrp =  
> ; Output frequency for trace(SD) and S to energy file  
> nstorireout = 100
> 
> ; Free energy variables  
> free-energy = no  
> couple-moltype =  
> couple-lambda0 = vdw-q  
> couple-lambda1 = vdw-q  
> couple-intramol = no  
> init-lambda = -1  
> init-lambda-state = -1  
> delta-lambda = 0  
> nstdhdl = 50  
> fep-lambdas =  
> mass-lambdas =  
> coul-lambdas =  
> vdw-lambdas =  
> bonded-lambdas =  
> restraint-lambdas =  
> temperature-lambdas =  
> calc-lambda-neighbors = 1  
> init-lambda-weights =  
> dhdl-print-energy = no  
> sc-alpha = 0  
> sc-power = 1  
> sc-r-power = 6  
> sc-sigma = 0.3  
> sc-coul = no  
> separate-dhdl-file = yes  
> dhdl-derivatives = yes  
> dh\_hist\_size = 0  
> dh\_hist\_spacing = 0.1
> 
> ; Non-equilibrium MD stuff  
> acc-grps =  
> accelerate =  
> freezegrps =  
> freezedim =  
> cos-acceleration = 0  
> deform =
> 
> ; simulated tempering variables  
> simulated-tempering = no  
> simulated-tempering-scaling = geometric  
> sim-temp-low = 300  
> sim-temp-high = 300
> 
> ; Electric fields  
> ; Format is number of terms (int) and for all terms an amplitude (real)  
> ; and a phase angle (real)  
> E-x =  
> ; Time dependent (pulsed) electric field. Format is omega, time for pulse  
> ; peak, and sigma (width) for pulse. Sigma = 0 removes pulse, leaving  
> ; the field to be a cosine function.  
> E-xt =  
> E-y =  
> E-yt =  
> E-z =  
> E-zt =
> 
> ; Ion/water position swapping for computational electrophysiology setups  
> ; Swap positions along direction: no, X, Y, Z  
> swapcoords = no  
> adress = no
> 
> ; User defined thingies  
> user1-grps =  
> user2-grps =  
> userint1 = 0  
> userint2 = 0  
> userint3 = 0  
> userint4 = 0  
> userreal1 = 0  
> userreal2 = 0  
> userreal3 = 0  
> userreal4 = 0

running that script triggers an error about deprecated Group value for cutoff-scheme option. When trying to switch cutoff-scheme from Group to Verlet, I get another error telling that Verlet option must be used with pbc option set to either xyz or xy. However, I want to perform this first minimization step in vacuum before generating any solvation box. Would you know how to make this script work with gromcas 2020 ?

thanks a lot

Eric

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<div class="post-metadata">

**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\
**Post date:** [May 11, 2020, 11:29pm UTC](https://gromacs.bioexcel.eu/t/minimization-in-vacuum-without-pbc/110/2 "2020-05-11T23:29:19Z")

</div>

You can run a vacuum simulation with PBC on, on the pro-visor that you don’t have pressure coupling turned on i.e. not NPT.

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<div class="post-metadata">

**Author:** ![cblau](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cblau/32/5_2.png) [@cblau](https://gromacs.bioexcel.eu/u/cblau)\
**Post date:** [May 12, 2020, 12:48pm UTC](https://gromacs.bioexcel.eu/t/minimization-in-vacuum-without-pbc/110/3 "2020-05-12T12:48:46Z")

</div>

The group scheme has been completely removed in GROMACS 2020 and with it the ability to use non-pbc simulations.

In practice, this won’t affect your, because you can still create a large box around your system and run the minimization with pbc as mentioned in the previous reply. The setup script should just work for this case once you use the Verlet scheme.

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [May 12, 2020, 1:00pm UTC](https://gromacs.bioexcel.eu/t/minimization-in-vacuum-without-pbc/110/4 "2020-05-12T13:00:19Z")

</div>

@cblau is there a plan to implement this feature? The ability to easily do vacuum simulations without PBC is really important, especially for force field work.

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<div class="post-metadata">

**Author:** ![cblau](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cblau/32/5_2.png) [@cblau](https://gromacs.bioexcel.eu/u/cblau)\
**Post date:** [May 12, 2020, 1:09pm UTC](https://gromacs.bioexcel.eu/t/minimization-in-vacuum-without-pbc/110/5 "2020-05-12T13:09:39Z")

</div>

It’s not high on the agenda, I just created an issue on gitlab to link this discussion back to development here

> **[Enable vacuum simulations (#3526) · Issues · GROMACS / GROMACS](https://gitlab.com/gromacs/gromacs/-/issues/3526)**
>
> For force-field parametrization work, easily running energy minimisations of compounds in vacuum is preferable. Some pipelines have broken due to the removal of the group scheme and subsequent inability to...

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<div class="post-metadata">

**Author:** ![ericpellegrini](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ericpellegrini/32/43_2.png) [@ericpellegrini](https://gromacs.bioexcel.eu/u/ericpellegrini)\
**Post date:** [May 12, 2020, 1:34pm UTC](https://gromacs.bioexcel.eu/t/minimization-in-vacuum-without-pbc/110/6 "2020-05-12T13:34:37Z")

</div>

ok thanks all for your help

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<div class="post-metadata">

**Author:** ![Neena](https://avatars.discourse-cdn.com/v4/letter/n/bc79bd/32.png) [@Neena](https://gromacs.bioexcel.eu/u/Neena)\
**Post date:** [May 17, 2020, 12:02am UTC](https://gromacs.bioexcel.eu/t/minimization-in-vacuum-without-pbc/110/7 "2020-05-17T00:02:32Z")

</div>

Try the below minimization parameters which has worked well for vacuum simulations. Proper way to do vacuum simulations: no PBC, PME and cutoffs. To reduce computation time, Konermann Lab solved it by implementing pseudo-PBC conditions. Their paper explains it very clearly (link here): [https://www.ncbi.nlm.nih.gov/pubmed/29678588](https://www.ncbi.nlm.nih.gov/pubmed/29678588)  
 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/9dff8d721af629ce81c9ad8cbecb8203d95dd77e.png)

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<div class="post-metadata">

**Author:** ![ericpellegrini](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ericpellegrini/32/43_2.png) [@ericpellegrini](https://gromacs.bioexcel.eu/u/ericpellegrini)\
**Post date:** [May 18, 2020, 9:32am UTC](https://gromacs.bioexcel.eu/t/minimization-in-vacuum-without-pbc/110/8 "2020-05-18T09:32:42Z")

</div>

thanks a lot for the settings. I will try them asap.

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<div class="post-metadata">

**Author:** ![sadaf](https://avatars.discourse-cdn.com/v4/letter/s/77aa72/32.png) [@sadaf](https://gromacs.bioexcel.eu/u/sadaf)\
**Post date:** [May 16, 2021, 4:58pm UTC](https://gromacs.bioexcel.eu/t/minimization-in-vacuum-without-pbc/110/9 "2021-05-16T16:58:56Z")

</div>

Dear All  
I am running with the same problem while doing a simulation of ligand in a vacuum. Dear @Neena could you please elaborate a little about setting these parameters as I am thinking of setting a simulation in a vacuum that should not have any neighboring interaction ( I am new to this any please correct me where I am wrong). I am trying to do grompp with the following parameters:-  
; minim.mdp - used as input into grompp to generate em.tpr  
; Parameters describing what to do, when to stop and what to save  
integrator = steep ; Algorithm (steep = steepest descent minimization)  
emtol = 1000.0 ; Stop minimization when the maximum force \< 1000.0 kJ/mol/nm  
emstep = 0.01 ; Minimization step size  
nsteps = 50000 ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions  
nstlist = 0 ; Frequency to update the neighbor list and long range forces  
cutoff-scheme = Verlet ; Buffered neighbor searching  
ns\_type = simple ; Method to determine neighbor list (simple, grid)  
coulombtype = cutoff ; Treatment of long range electrostatic interactions  
rcoulomb = 0.0 ; Short-range electrostatic cut-off  
rvdw = 0.0 ; Short-range Van der Waals cut-off  
constraints = none ; Bond types to replace by constraints  
pbc = yes ; Periodic Boundary Conditions in all 3 dimensions

But I am getting a segmentation fault core dumped error. How should I select these parameters to do a vacuum simulation?  
Regards  
Sadaf

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<div class="post-metadata">

**Author:** ![Neena](https://avatars.discourse-cdn.com/v4/letter/n/bc79bd/32.png) [@Neena](https://gromacs.bioexcel.eu/u/Neena)\
**Post date:** [May 17, 2021, 1:58am UTC](https://gromacs.bioexcel.eu/t/minimization-in-vacuum-without-pbc/110/10 "2021-05-17T01:58:17Z")

</div>

Hi Sadaf,

Proper way to do vacuum simulations: no PBC, PME and cutoffs (with nstlist=0). To reduce computation time, Konermann Lab solved it by implementing pseudo-PBC conditions. Basically, molecule is prepared in a very large periodic box (333.3 nm infinite cut offs - essentially no cut off) such that it remains isolated. Their paper explains it very clearly (link here): [[https://www.ncbi.nlm.nih.gov/pubmed/29678588](https://www.ncbi.nlm.nih.gov/pubmed/29678588) ]  
Below is my minim.mdp file:  
 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/6c663501a6298034a1e18477d2bc30d55474745b.png)  
Note: I used ns\_type: grid since I was simulating a protein

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<div class="post-metadata">

**Author:** ![sadaf](https://avatars.discourse-cdn.com/v4/letter/s/77aa72/32.png) [@sadaf](https://gromacs.bioexcel.eu/u/sadaf)\
**Post date:** [May 18, 2021, 8:26am UTC](https://gromacs.bioexcel.eu/t/minimization-in-vacuum-without-pbc/110/11 "2021-05-18T08:26:24Z")

</div>

Dear @Neena  
Thank you very much for your kind reply.  
I am working on the ligand simulation in vacuum. I build topology and a box of 100nm around the ligand as below:-  
gmx editconf -f NAP.gro -o NAPbox.gro -c -d 100.0 -bt cubic  
followed by:-  
gmx grompp -f minim.mdp -c NAPbox.gro -p topol.top -o NAP.tpr  
However when I do:-  
gmx mdrun -v -deffnm em  
I get the following error:-  
Program: gmx mdrun, version 2021  
Source file: src/gromacs/options/options.cpp (line 179)  
Function: void gmx::internal::OptionSectionImpl::finish()

Error in user input:  
Invalid input values  
In option s  
Required option was not provided, and the default file ‘topol’ does not  
exist or is not accessible.  
The following extensions were tried to complete the file name:  
.tpr  
I have NAP.tpr in my working directory.

I have following parameters in my minim.mdp file:-  
; minim.mdp - used as input into grompp to generate em.tpr  
; Parameters describing what to do, when to stop and what to save  
integrator = steep ; Algorithm (steep = steepest descent minimization)  
emtol = 1000.0 ; Stop minimization when the maximum force \< 1000.0 kJ/mol/nm  
emstep = 0.01 ; Minimization step size  
nsteps = 50000 ; Maximum number of (minimization) steps to perform  
nstxout = 100  
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions  
nstlist = 1 ; Frequency to update the neighbor list and long range forces  
cutoff-scheme = Verlet ; Buffered neighbor searching  
ns\_type = grid ; Method to determine neighbor list (simple, grid)  
coulombtype = cutoff ; Treatment of long range electrostatic interactions  
rcoulomb = 100 ; Short-range electrostatic cut-off  
rvdw = 100 ; Short-range Van der Waals cut-off  
constraints = none ; Bond types to replace by constraints  
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions  
rlist =100 ; Short range neighbour list cutoff

I tried with your provided settings but getting same error. Could you please suggest me how should I fix this error?  
Regards  
Sadaf

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<div class="post-metadata">

**Author:** ![pjohansson](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pjohansson/32/316_2.png) [@pjohansson](https://gromacs.bioexcel.eu/u/pjohansson)\
**Post date:** [May 18, 2021, 10:11am UTC](https://gromacs.bioexcel.eu/t/minimization-in-vacuum-without-pbc/110/12 "2021-05-18T10:11:52Z")

</div>

Hi,

since you specify `-deffnm em` which sets default file names to `em.[extension]`, `mdrun` is looking for a file called `em.tpr`.

You need to specify _your_ file with `-s NAP.tpr`.

Regards,  
Petter

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<div class="post-metadata">

**Author:** ![sadaf](https://avatars.discourse-cdn.com/v4/letter/s/77aa72/32.png) [@sadaf](https://gromacs.bioexcel.eu/u/sadaf)\
**Post date:** [May 19, 2021, 5:38am UTC](https://gromacs.bioexcel.eu/t/minimization-in-vacuum-without-pbc/110/13 "2021-05-19T05:38:03Z")

</div>

Thank you  
@pjohansson @Neena it worked  
Regards  
Sadaf

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**Author:** ![sadaf](https://avatars.discourse-cdn.com/v4/letter/s/77aa72/32.png) [@sadaf](https://gromacs.bioexcel.eu/u/sadaf)\
**Post date:** [May 23, 2021, 2:48pm UTC](https://gromacs.bioexcel.eu/t/minimization-in-vacuum-without-pbc/110/14 "2021-05-23T14:48:06Z")

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Dear All  
I want to switch off non-bonded interaction completely so that there would be no intramolecular interaction as well for which I followed as mentioned above. However, I get 1-4 Lenard Jones and Coulombic interactions in the log file still.  
Step Time  
0 0.00000

Energies (kJ/mol)  
Bond Angle Proper Dih. LJ-14 Coulomb-14  
3.06426e+02 2.25654e+02 2.65055e+02 1.87424e+02 -2.24481e+03  
LJ (SR) Coulomb (SR) Potential Pressure (bar)  
0.00000e+00 -1.52038e+06 -1.52164e+06 5.25943e-03

How should I set the system so that there come no LJ-14 and Coulomb-14 interactions?  
Regards  
Sadaf

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<div class="post-metadata">

**Author:** ![mj.rezayani](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mj.rezayani/32/3918_2.png) [@mj.rezayani](https://gromacs.bioexcel.eu/u/mj.rezayani)\
**Post date:** [July 17, 2021, 11:57am UTC](https://gromacs.bioexcel.eu/t/minimization-in-vacuum-without-pbc/110/15 "2021-07-17T11:57:54Z")

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Dear Neena

Hi,

How can I change this parameters defined in min.mdp for nvt.mdp? I’d like to simulate my polymer system in NVT level but I am not sure how to change it.

Thanks a lot