GROMACS version:2023

GROMACS modification: No

I’m doing something dumb.

My remd.mdp file contains these entries:

; Electrostatics

coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics

pme_order = 4 ; cubic interpolation

fourierspacing = 0.16 ; grid spacing for FFT

continuation = yes ; Restarting after equilibration

constraint_algorithm = lincs ; holonomic constraints

constraints = h-bonds ; bonds involving H are constrained

lincs_iter = 1 ; accuracy of LINCS

lincs_order = 4 ; also related to accuracy

When I run this script from the directory containing my remd.mdp file:

#!/bin/bash

mdpFile=./remd.mdp

while read replica temp

do

sed -e ’s/TEMP/’$temp’/g’ $mdpFile > rep_$replica.mdp

gmx grompp -f rep_$replica.mdp -c IV.gro -p IV.top -o IV_$replica.tpr

done

It returns the expected 16 tpr files, but with 4 notes:

- for a correct single point energy eval with nsteps = 0 use continuation = yes
- atoms 24 OG1 and 25HG1 have a period < 10x step time, maybe you forgot to change the constraints mdp option?
- simulation will use initial temp of 299.33 K for determining Verlet buffer size (none of the 16 temps are 299.33 and this note and same temperature is output for all replicas.
- You are using a plain Coulomb cut-off… consider PME…

I suspect I’ve made a stupid mistake in the script, because the instructions in the remd.mdp file don’t seem to be coming through. The mdout.mdp has, e.g.:

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype = Cut-off

coulomb-modifier = Potential-shift-Verlet

rcoulomb-switch = 0

rcoulomb = 1

Is my script wrong? That’s my best guess, although I don’t know how grompp is generating the wrong mdp values out of thin air. This is a test to check the acceptance ratio between the replicas. The whole mdp file follows.

Thank you for any and all help.

Best,

Ken

;title = OPLS REMDtest ns run TIV

; Run parameters

integrator = md ; leap-frog integrator

nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns)

dt = 0.002 ; 2 fs

; Output control

nstxout = 0 ; suppress bulky .trr file by specifying

nstvout = 0 ; 0 for output frequency of nstxout,

nstfout = 0 ; nstvout, and nstfout

nstenergy = 5000 ; save energies every 10.0 ps

nstlog = 5000 ; update log file every 10.0 ps

nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps

compressed-x-grps = System ; save the whole system

; Bond parameters

continuation = yes ; Restarting after NPT

constraint_algorithm = lincs ; holonomic constraints

constraints = h-bonds ; bonds involving H are constrained

lincs_iter = 1 ; accuracy of LINCS

lincs_order = 4 ; also related to accuracy

; Neighborsearching

cutoff-scheme = Verlet ; Buffered neighbor searching

ns_type = grid ; search neighboring grid cells

nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme

rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)

rvdw = 1.0 ; short-range van der Waals cutoff (in nm)

; Electrostatics

coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics

pme_order = 4 ; cubic interpolation

fourierspacing = 0.16 ; grid spacing for FFT

; Temperature coupling is on

tcoupl = V-rescale ; modified Berendsen thermostat

tc-grps = Protein Non-Protein ; two coupling groups - more accurate

tau_t = 0.1 0.1 ; time constant, in ps

ref_t = TEMP TEMP ; reference temperature, one for each group, in K

; Pressure coupling is on

pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT

pcoupltype = isotropic ; uniform scaling of box vectors

tau_p = 2.0 ; time constant, in ps

ref_p = 1.0 ; reference pressure, in bar

compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1

; Periodic boundary conditions

pbc = xyz ; 3-D PBC

; Dispersion correction

DispCorr = EnerPres ; account for cut-off vdW scheme

; Velocity generation

gen_vel = no ; Velocity generation is off