thank you so much,
i try , pull rate= 0.005 ;0.005 nm per ps = 5 nm per ns for nsteps = 500000 ; 1000 ps (1ns).
can you pls suggest me, is there any particular minimum pull rate.
for protein and ligand to create summary.dat file
in the script
gmx distance -s pull.tpr -f conf${i}.gro -n index.ndx -select ‘com of group “protein” plus com of group “lig”’ -oall dist${i}.xvg
command not working , while using the script i got the following error
Invalid index group reference(s)
Cannot match ‘group “lig”’, because no such index group can be found.
i created the index group for protein_ligand using this command gmx make_ndx -f npt.gro
because i used tc_grps = Protein_lig Water_and_ions
There’s no minimum pull rate. In general, I think it’s better to pull a bit too slowly than too fast. But the pulling simulation will, of course, take longer then.
If you haven’t created a “lig” group you can’t use that group in gmx distance. If you try without the -select option I think you will get a list of groups. There is probably one that will contain the ligand, look for its molecule type name.
Command line:
gmx_mpi distance -s pull.tpr -f conf0.gro -n index.ndx -oall dist0.xvg
Available static index groups:
Group 0 “System” (76362 atoms)
Group 1 “Protein” (3283 atoms)
Group 2 “Protein-H” (1706 atoms)
Group 3 “C-alpha” (221 atoms)
Group 4 “Backbone” (663 atoms)
Group 5 “MainChain” (883 atoms)
Group 6 “MainChain+Cb” (1079 atoms)
Group 7 “MainChain+H” (1097 atoms)
Group 8 “SideChain” (2186 atoms)
Group 9 “SideChain-H” (823 atoms)
Group 10 “Prot-Masses” (3283 atoms)
Group 11 “non-Protein” (73079 atoms)
Group 12 “Other” (52 atoms)
Group 13 “lig” (52 atoms)
Group 14 “NA” (60 atoms)
Group 15 “CL” (49 atoms)
Group 16 “Water” (72918 atoms)
Group 17 “SOL” (72918 atoms)
Group 18 “non-Water” (3444 atoms)
Group 19 “Ion” (109 atoms)
Group 20 “lig” (52 atoms)
Group 21 “NA” (60 atoms)
Group 22 “CL” (49 atoms)
Group 23 “Water_and_ions” (73027 atoms)
Group 24 “protein_lig” (3335 atoms)
Specify any number of selections for option ‘select’
(Position pairs to calculate distances for):
(one per line, for status/groups, ‘help’ for help, Ctrl-D to end)
1
Selection ‘1’ parsed
13
Selection ‘13’ parsed
Reading file pull.tpr, VERSION 2019.4 (single precision)
Reading file pull.tpr, VERSION 2019.4 (single precision)
Program: gmx distance, version 2019.4
Source file: src/gromacs/trajectoryanalysis/modules/distance.cpp (line 204)
Function: void gmx::analysismodules::{anonymous}::checkSelections(const SelectionList&)
Inconsistency in user input:
Selection ‘Protein’ does not evaluate into an even number of positions (there
are 3283 positions)
how to solve this issue
gmx distance calculates pairwise distances in a group. The selection expression you had above was apparently (trying) to make a pair of the two COMs. I’m not sure why that didn’t work, since you seem to have a “lig” selection group. From where did you get the syntax for that -select input?
Is there a reason why you need gmx distance at all? Why not use the pullx.xvg output?
in the tutorial (Umbrella Sampling) mentioned to find the distance. based on the tutorial i used gmx distance to calculate distance.
in the tutorial the mentioned to spacing of the windows generally 0.1 to 0.2 nm, shall instead of used gmx distance shall i use pullx.xvg to calcualte the distance and select the windows based on pullx.xvg.
spacing of the windows should be 0.1 to 0.2 nm maintained or greater than this spacing also can use?
can you suggest me pls and correct my mistake
I don’t see exactly why your gmx distance command didn’t work as in the tutorial. But for now, I guess it has to do with the groups in the index file.
It doesn’t really matter how you get the conformations for the umbrella sampling windows. It should be OK to use the pullx.xvg file.
The spacing is system dependent. Steep regions (or regions with high curvature) of the free energy landscape generally requires higher pull force constants and tighter umbrella window placement. A greater spacing than 0.2 nm might be possible to use in the aqueous regions, when the PMF is expected to be flat. But I think 0.2 nm is probably good there and significantly tighter (possibly a lot tighter than 0.1 nm) in more “problematic” regions. If you would like to start with the umbrella windows distributed evenly (and possibly add more where the histogram overlap is insufficient), I would suggest a spacing of 0.1 to 0.15 nm to start with.
Thank you .
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Initialized rapid wham stuff (contrib tolerance 9.09091e-08)
Evaluating only 412 of 2200 expressions.
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31300) Maximum change 2.638265e-06
31400) Maximum change 2.626677e-06
31500) Maximum change 2.615140e-06
31600) Maximum change 2.603655e-06
31700) Maximum change 2.592220e-06
31800) Maximum change 2.580836e-06
31900) Maximum change 2.569503e-06
32000) Maximum change 2.558221e-06
32100) Maximum change 2.546988e-06
32200) Maximum change 2.535805e-06
32300) Maximum change 2.524672e-06
32400) Maximum change 2.513589e-06
32500) Maximum change 2.502554e-06
32600) Maximum change 2.491569e-06
32700) Maximum change 2.480632e-06
32800) Maximum change 2.469744e-06
32900) Maximum change 2.458905e-06
33000) Maximum change 2.448113e-06
33100) Maximum change 2.437369e-06
33200) Maximum change 2.426673e-06
33300) Maximum change 2.416024e-06
33400) Maximum change 2.405423e-06
33500) Maximum change 2.394868e-06
33600) Maximum change 2.384361e-06
33700) Maximum change 2.373900e-06
33800) Maximum change 2.363485e-06
33900) Maximum change 2.353116e-06
34000) Maximum change 2.342794e-06
34100) Maximum change 2.332517e-06
34200) Maximum change 2.322286e-06
34300) Maximum change 2.312100e-06
34400) Maximum change 2.301959e-06
34500) Maximum change 2.291863e-06
34600) Maximum change 2.281811e-06
34700) Maximum change 2.271805e-06
34800) Maximum change 2.261842e-06
34900) Maximum change 2.251924e-06
35000) Maximum change 2.242050e-06
35100) Maximum change 2.232219e-06
35200) Maximum change 2.222432e-06
35300) Maximum change 2.212688e-06
35400) Maximum change 2.202987e-06
35500) Maximum change 2.193329e-06
35600) Maximum change 2.183714e-06
35700) Maximum change 2.174141e-06
35800) Maximum change 2.164611e-06
35900) Maximum change 2.155123e-06
36000) Maximum change 2.145677e-06
36100) Maximum change 2.136272e-06
36200) Maximum change 2.126910e-06
36300) Maximum change 2.117588e-06
36400) Maximum change 2.108308e-06
36500) Maximum change 2.099069e-06
36600) Maximum change 2.089871e-06
36700) Maximum change 2.080713e-06
36800) Maximum change 2.071596e-06
36900) Maximum change 2.062519e-06
37000) Maximum change 2.053482e-06
37100) Maximum change 2.044485e-06
37200) Maximum change 2.035528e-06
37300) Maximum change 2.026610e-06
37400) Maximum change 2.017732e-06
37500) Maximum change 2.008893e-06
37600) Maximum change 2.000093e-06
37700) Maximum change 1.991332e-06
37800) Maximum change 1.982609e-06
37900) Maximum change 1.973925e-06
38000) Maximum change 1.965279e-06
38100) Maximum change 1.956672e-06
38200) Maximum change 1.948103e-06
38300) Maximum change 1.939571e-06
38400) Maximum change 1.931077e-06
38500) Maximum change 1.922620e-06
38600) Maximum change 1.914201e-06
38700) Maximum change 1.905819e-06
38800) Maximum change 1.897474e-06
38900) Maximum change 1.889165e-06
39000) Maximum change 1.880894e-06
39100) Maximum change 1.872659e-06
39200) Maximum change 1.864460e-06
39300) Maximum change 1.856297e-06
39400) Maximum change 1.848170e-06
39500) Maximum change 1.840079e-06
39600) Maximum change 1.832024e-06
39700) Maximum change 1.824004e-06
39800) Maximum change 1.816020e-06
39900) Maximum change 1.808071e-06
40000) Maximum change 1.800156e-06
40100) Maximum change 1.792277e-06
40200) Maximum change 1.784432e-06
40300) Maximum change 1.776622e-06
40400) Maximum change 1.768847e-06
40500) Maximum change 1.761105e-06
40600) Maximum change 1.753398e-06
40700) Maximum change 1.745725e-06
40800) Maximum change 1.738085e-06
40900) Maximum change 1.730479e-06
41000) Maximum change 1.722907e-06
41100) Maximum change 1.715368e-06
41200) Maximum change 1.707862e-06
41300) Maximum change 1.700389e-06
41400) Maximum change 1.692950e-06
41500) Maximum change 1.685542e-06
41600) Maximum change 1.678168e-06
41700) Maximum change 1.670826e-06
41800) Maximum change 1.663516e-06
41900) Maximum change 1.656238e-06
42000) Maximum change 1.648993e-06
42100) Maximum change 1.641779e-06
42200) Maximum change 1.634597e-06
42300) Maximum change 1.627447e-06
42400) Maximum change 1.620328e-06
42500) Maximum change 1.613240e-06
42600) Maximum change 1.606184e-06
42700) Maximum change 1.599159e-06
42800) Maximum change 1.592164e-06
42900) Maximum change 1.585200e-06
43000) Maximum change 1.578267e-06
43100) Maximum change 1.571365e-06
43200) Maximum change 1.564493e-06
43300) Maximum change 1.557651e-06
43400) Maximum change 1.550839e-06
43500) Maximum change 1.544057e-06
43600) Maximum change 1.537305e-06
43700) Maximum change 1.530582e-06
43800) Maximum change 1.523889e-06
43900) Maximum change 1.517226e-06
44000) Maximum change 1.510592e-06
44100) Maximum change 1.503986e-06
44200) Maximum change 1.497410e-06
44300) Maximum change 1.490863e-06
44400) Maximum change 1.484345e-06
44500) Maximum change 1.477855e-06
44600) Maximum change 1.471394e-06
44700) Maximum change 1.464961e-06
44800) Maximum change 1.458557e-06
44900) Maximum change 1.452180e-06
45000) Maximum change 1.445832e-06
45100) Maximum change 1.439511e-06
45200) Maximum change 1.433219e-06
45300) Maximum change 1.426954e-06
45400) Maximum change 1.420716e-06
45500) Maximum change 1.414506e-06
45600) Maximum change 1.408323e-06
45700) Maximum change 1.402167e-06
45800) Maximum change 1.396038e-06
45900) Maximum change 1.389937e-06
46000) Maximum change 1.383862e-06
46100) Maximum change 1.377813e-06
46200) Maximum change 1.371791e-06
46300) Maximum change 1.365796e-06
46400) Maximum change 1.359827e-06
46500) Maximum change 1.353884e-06
46600) Maximum change 1.347967e-06
46700) Maximum change 1.342077e-06
46800) Maximum change 1.336212e-06
46900) Maximum change 1.330373e-06
47000) Maximum change 1.324559e-06
47100) Maximum change 1.318771e-06
47200) Maximum change 1.313008e-06
47300) Maximum change 1.307271e-06
47400) Maximum change 1.301559e-06
47500) Maximum change 1.295872e-06
47600) Maximum change 1.290209e-06
47700) Maximum change 1.284572e-06
47800) Maximum change 1.278959e-06
47900) Maximum change 1.273371e-06
48000) Maximum change 1.267808e-06
48100) Maximum change 1.262269e-06
48200) Maximum change 1.256754e-06
48300) Maximum change 1.251264e-06
48400) Maximum change 1.245797e-06
48500) Maximum change 1.240355e-06
48600) Maximum change 1.234936e-06
48700) Maximum change 1.229541e-06
48800) Maximum change 1.224170e-06
48900) Maximum change 1.218822e-06
49000) Maximum change 1.213498e-06
49100) Maximum change 1.208197e-06
49200) Maximum change 1.202919e-06
49300) Maximum change 1.197665e-06
49400) Maximum change 1.192433e-06
49500) Maximum change 1.187225e-06
49600) Maximum change 1.182039e-06
49700) Maximum change 1.176876e-06
49800) Maximum change 1.171736e-06
49900) Maximum change 1.166618e-06
50000) Maximum change 1.161523e-06
50100) Maximum change 1.156450e-06
50200) Maximum change 1.151399e-06
50300) Maximum change 1.146370e-06
50400) Maximum change 1.141364e-06
50500) Maximum change 1.136379e-06
50600) Maximum change 1.131416e-06
50700) Maximum change 1.126475e-06
50800) Maximum change 1.121556e-06
50900) Maximum change 1.116658e-06
51000) Maximum change 1.111781e-06
51100) Maximum change 1.106926e-06
51200) Maximum change 1.102092e-06
51300) Maximum change 1.097280e-06
51400) Maximum change 1.092488e-06
51500) Maximum change 1.087718e-06
51600) Maximum change 1.082968e-06
51700) Maximum change 1.078239e-06
51800) Maximum change 1.073531e-06
51900) Maximum change 1.068844e-06
52000) Maximum change 1.064177e-06
52100) Maximum change 1.059530e-06
52200) Maximum change 1.054904e-06
52300) Maximum change 1.050298e-06
52400) Maximum change 1.045712e-06
52500) Maximum change 1.041147e-06
52600) Maximum change 1.036601e-06
52700) Maximum change 1.032075e-06
52800) Maximum change 1.027569e-06
52900) Maximum change 1.023083e-06
53000) Maximum change 1.018617e-06
53100) Maximum change 1.014170e-06
53200) Maximum change 1.009742e-06
53300) Maximum change 1.005334e-06
53400) Maximum change 1.000945e-06
Switched to exact iteration in iteration 53422
Converged in 53423 iterations. Final maximum change 9.99938e-07
can you suggest me how to solve this. what mistakes i did
can you suggest me how to solve this issue
You’re missing samples in the regions specified by the warning messages: where there are flat regions in the PMF. Check the distribution of input configurations when you start the umbrella simulations.
As before, make sure that you have a high enough force constant when you are pulling, to generate the umbrella sampling input configurations, and make sure that you save coordinates often enough to have a good coverage of the whole region you are interested in.
If there are input coordinates in those regions then your force constants during the umbrella simulations are too low.
i got the pullx.xvg , is it correct
pullx.xvg (82.8 KB)