Re: [gmx-users] Help with gmx make_ndx

It is difficult to understand what is the problem from your mail. if you are unable to use make_ndx try as follows Copy the atoms you wanted to make as one group manually create a group name and paste it. You have to take care the mdp options such as energy groups and t-coupling -- Gromacs Users

Re: [gmx-users] Help with gmx make_ndx

Mark Abraham: > If you want to engage in discussion, please don't subscribe to the digest > and then reply to its emails. That makes it painful for everyone to follow > the discussion. I'm very sorry for my stupid ( I am new to mailing list so not familiar with reply) >> I think if I type 8|9

Re: [gmx-users] unknown bond atom_type +

Hi, You can upload files to any file-sharing service and share links, but the list doesn't accept attachments to send to thousands of people. More importantly, your .rtp files are inputs for pdb2gmx, not grompp, so something about your reporting doesn't make sense. But we still can't see your

Re: [gmx-users] unknown bond atom_type +

May I upload my input and output files? solving this problem is really critical for me. thanks, On 8/24/16, SAKO MIRZAIE wrote: > I have added the following residue to rtp: > [ PES ] > [ atoms ] >H1HO 0.405002 1 >O1OH -0.603301

Re: [gmx-users] unknown bond atom_type +

I have added the following residue to rtp: [ PES ] [ atoms ] H1HO 0.405002 1 O1OH -0.603301 2 C1CT 0.127400 3 C2CT 0.130400 4 H2H1 0.035700 5 H3H1 0.035700 6 H4HC

Re: [gmx-users] unknown bond atom_type +

sorry, I made a mistake, the output is mdout.mdp. maybe I should try the gromacs 5. I also tried to run a martini md on it. but when I employed polarize water, in minimization step, I got a lot of LINKS errors. now, I come back to atomistic md, and hope to solve it. On 8/24/16, Mark Abraham

Re: [gmx-users] CPU running doesn't match command line

On Wed, Aug 24, 2016 at 1:03 AM, Szilárd Páll wrote: > On Mon, Aug 22, 2016 at 5:36 PM, Albert wrote: >> Hello Mark: >> >> I've recompiled Gromacs without MPI. I run submit the job with the command >> line you suggested. >> >> gmx mdrun -ntomp 10 -v

Re: [gmx-users] unknown bond atom_type +

Hi, You should really not be starting new work with ancient no-longer-supported code versions... Running grompp on the server is typically not a great idea. What is the full output that grompp writes to the terminal? Hint, it is unlikely to be called em_out.log, which might be a file you wrote

Re: [gmx-users] CPU running doesn't match command line

On Mon, Aug 22, 2016 at 5:36 PM, Albert wrote: > Hello Mark: > > I've recompiled Gromacs without MPI. I run submit the job with the command > line you suggested. > > gmx mdrun -ntomp 10 -v -g test.log -pin on -pinoffset 0 -gpu_id 0 -s > test.tpr >& test.info > gmx mdrun

Re: [gmx-users] REST2 swapping/exchange implementation in GROMACS

Hi, Just as with temperature REM, at the intervals you choose, the simulation will stop and adjacent replicas will do a Metropolis check for whether their configurations are representative of the conditions in the other simulations. The principle is independent of what varies across replicas.

Re: [gmx-users] unknown bond atom_type +

I am using gromacs 4.5. my grompp input files are just topology and a gro file. neither of them have "+". when I add the "+" to the ffnonbonded file with wrong parameters, it error is disappeared. I am really confused. I am using a server for my simulations and the em_out.log lacks the error.

Re: [gmx-users] REST2 swapping/exchange implementation in GROMACS

Dear Mark, Sorry about posting in the wrong mailing list. I understand that when implementing REST2 in GROMACS I am generating replicas through various lambdas. These replicas will run at same temperature say at 300 K and will only have an "effective temperature". [a-The lambdas will vary from

Re: [gmx-users] unknown bond atom_type +

Hi, Please keep discussion on the list. I can only suggest you going looking for the + symbol in your grompp inputs, because you've only shared a tiny fraction of your information... like the whole grompp output (or at least error message without copy-paste typos), and your GROMACS version.

Re: [gmx-users] Help with gmx make_ndx

Hi, If you want to engage in discussion, please don't subscribe to the digest and then reply to its emails. That makes it painful for everyone to follow the discussion. Quyen said: > thanks for your replying, > I think if I type 8|9 then my index.ndx should not appear [systems] group ( > it too

Re: [gmx-users] mdrun not working

Hi, Sounds like you'd better ask the authors of that patch whether it supports checkpoint restart, or how they recommend you to restart. Mark On Tue, Aug 23, 2016 at 7:25 PM vivek naik wrote: > I did all the disk cleaning. Now it has more than enough space... > >

Re: [gmx-users] REST2 swapping/exchange implementation in GROMACS

Hi, Please do not post questions about how to use GROMACS to the gmx-developers mailing list, which is for questions about how to write code related to GROMACS. On Tue, Aug 23, 2016 at 8:29 PM shivangi nangia wrote: > Hello, > > I have a question regarding

Re: [gmx-users] unknown bond atom_type +

Hi, The full version, I should say. Mark On Tue, 23 Aug 2016 23:54 Mark Abraham wrote: > Hi, > > Does the future version of the error message suggest a line number for you > to look at? > > Mark > > On Tue, 23 Aug 2016 23:11 SAKO MIRZAIE

Re: [gmx-users] unknown bond atom_type +

Hi, Does the future version of the error message suggest a line number for you to look at? Mark On Tue, 23 Aug 2016 23:11 SAKO MIRZAIE wrote: > Dear All, > > I am trying to do vacuum md on a huge polymer, f-127. I had to add sex > residues to rtp file, but with know

[gmx-users] unknown bond atom_type +

Dear All, I am trying to do vacuum md on a huge polymer, f-127. I had to add sex residues to rtp file, but with know atom types. now, when I run the grompp, I got the following error: "unknown bond atom_type +" I checked my topology file and I have no any atom named "+". I don't know what does

Re: [gmx-users] REST2 swapping/exchange implementation in GROMACS

Dear SNX: This is just a suggestion: may be youn can modify the part decide wheather to take a replic exchange in the src/kernel/repl_ex.c ? In v 4.6.5 it is in line ~180-200. May be use plumed would be a easier way? (I'm currently using solid templing in plumed hrex version + gromacs 4.6.7)

[gmx-users] REST2 swapping/exchange implementation in GROMACS

Hello, I have a question regarding implementing REST2 in GROMACS as suggested in: ( On easy implementation of a variant of the replica exchange with solute tempering in GROMACS, J Comput Chem. 32, 1228-1234, 2010). How does the gromacs machinery know how to carry out the exchange/swapping? the

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 148, Issue 88

thanks for your replying, I think if I type 8|9 then my index.ndx should not appear [systems] group ( it too large for my system) And if I use index of LA and CL in index.ndx to get coordinate from xtc file, I got message: Segmentation fault (core dumped) > Hi, > > What do you think is wrong

Re: [gmx-users] mdrun not working

I did all the disk cleaning. Now it has more than enough space... But mdrun seems to be stuck after starting at just the last point where the simulation is supposed to run. Vivek On Tue, Aug 23, 2016 at 10:10 PM, Mark Abraham wrote: > Hi, > > If the disk is full,

Re: [gmx-users] CPU running doesn't match command line

I use command line "top" to check how many CPUs are using. Each gmx occupied 7.5 CPU. On 08/23/2016 06:38 PM, Mark Abraham wrote: Hi, How did you decide that only 15 cores were being used? What performance did you observe with only one of the jobs running, vs the performance of both of

Re: [gmx-users] mdrun not working

Hi, If the disk is full, just starting mdrun again isn't going to help. mdrun needs to write to disk, so you need to free some space. Mark On Mon, Aug 22, 2016 at 11:11 AM vivek naik wrote: > Dear users, > > I was carrying out simulations using Gromacs-LS. It is a

Re: [gmx-users] NPT Equilbration fails

Hi, What box dimensions should be appropriate for the density of such a mixture? Mark On Mon, Aug 22, 2016 at 4:54 PM Apramita Chand wrote: > Dear All, > I'm trying to create a pre-equilbrated urea-water box to solvate my peptide > with, using GROMOS53a6 parameters.

Re: [gmx-users] CPU running doesn't match command line

Hi, How did you decide that only 15 cores were being used? What performance did you observe with only one of the jobs running, vs the performance of both of them while both are running? Please share log files via links to files on a file sharing service - it's quite tedious and inefficient if we

Re: [gmx-users] Running gromacs in parallel

Hi, The GROMACS log files will report whether they were built with MPI support, and how many ranks the MPI system told the GROMACS executable that were available. Assuming you've built with MPI support (rather than thread-MPI), then you'll need to read your slurm and cluster documentation to work

Re: [gmx-users] Help with gmx make_ndx

Hi, What do you think is wrong about the contents of the index group that was made? Mark On Tue, Aug 23, 2016 at 6:26 PM Quyen V. Vu wrote: > Dear gromacs user, > my system contain such groups: > > 0 System : 943920 atoms > 1 DNA : 3198

[gmx-users] Help with gmx make_ndx

Dear gromacs user, my system contain such groups: 0 System : 943920 atoms 1 DNA : 3198 atoms 2 LA :76 atoms 3 CL : 130 atoms 4 Water : 940516 atoms 5 SOL : 940516 atoms 6 non-Water

Re: [gmx-users] Remove PDB and center the protein.

If you want to remove the pbc, you must use -pbc nojump. -pbc mol will put everything in the pbc while having whole molecules (molecules not cut by the pbc), that's all. I probably don't get what you call "PBC removed" though. For the analysis, it depends on your system (and what you want to

Re: [gmx-users] Remove PDB and center the protein.

Hi, thanks for reply. If I understand correctly, one should not carry out multiple passes to achieve multiple conversions of trajectory. Here, I want both protein to be centered and PBC removed. So, instead of case 3, I did following and it keeps protein in the center. trjconv -s *.tpr -f *.xtc

Re: [gmx-users] Remove PDB and center the protein.

Hi, As http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions suggests, you may well need multiple passes of trjconv. The implementation hard-codes the order of operations when you try to run more than one in the same call to trjconv. If you want the "other" order, then you

Re: [gmx-users] Remove PDB and center the protein.

Hello, thank you all for helping. As mentioned in my question, 3rd case gives desired result that is centering protein with dodecahedron visualization. So my question is, why first two step fail that first centering and then removal of PBC and vice versa, both dont give right answer but

Re: [gmx-users] How to run a mpi command in gromacs 4.5 version

Hi, GROMACS 4.5 didn't support OpenMP, so what you're trying simply cannot work. Since you're trying to run in parallel, you're after good simulation performance, which means you should be installing and using the latest released version, particularly if you are starting new work. And in all

Re: [gmx-users] Remove PDB and center the protein.

Usually, what works most of the time (haven't failed yet with this) is first removing the PBC: gmx trjconv -s inp.tpr -f inp.xtc -o nopbc.xtc -pbc nojump And then centering: gmx trjconv -s inp.tpr -f nopbc.xtc -o nopbc_center.xtc -center If you later want the PBC back with the centered system,

Re: [gmx-users] Any update on constant pH simulation?

Hi Jagannath, The current implementation an older GROMACS version (3.3.1) can in principle be used, but is slow for systems with many titratable sites na d has some other restrictions. You find it here: http://www.mpibpc.mpg.de/grubmueller/constpH The new constant pH framework will offer

[gmx-users] How to run a mpi command in gromacs 4.5 version

Hi all, * command used :* *mpirun -np NP_tot mdrun_mpi -deffnm md -npme NP_pme -ntomp NT* *mpirun -np 11 mdrun_mpi -ntomp 2 -npme 6 -ntomp_pme 1* *comment which i am getting while running the mpi:* *mpirun was unable to launch the specified application as it could

Re: [gmx-users] Remove PDB and center the protein.

Hi, I did something similar last month for a protein tetramer solvated using a truncated dodecahedron ;) Hope the following will help gmx trjconv -s inp.tpr -f inp.xtc -o clust.xtc -center -pbc clust gmx trjconv -s inp.tpr -f clust.xtc -o ok.xtc -center -pbc mol -ur compact As simulating a

[gmx-users] Remove PDB and center the protein.

HI all, I have simulated protein in a dodecahedron box. I know trjconv can be used to center the protein and remove PBC but I am confused. I have tried few cases as follows. Case 1 trjconv -f *.xtc -s *.tpr -center -o centered.xtc trjconv -f centered.xtc -s *.tpr -pbc mol -ur compact -o