Re: [gmx-users] FEP calculations on multiple nodes

Okay, you might need to consider gmx mdrun -v -ntmpi XX -ntomp XX -deffnm -gpu_id XXX http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html

Re: [gmx-users] Average and bfactors.pdb

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Hi justin Thank you so much for replyingAccording to the gromacs tuturial, i am trying to analyse my complex in terms of RMSD. 

Re: [gmx-users] FEP calculations on multiple nodes

Hi, That's exactly the problem. There is no error except segmentation fault. I have provided the *.log file link below if that helps. https://filetea.me/n3wNaRevmeUS8iFWrIs4UlHfQ On 21 August 2017 at 19:12, Nikhil Maroli wrote: > Hi, > > Where and What is the error? It

[gmx-users] Trouble with gmx distance

Hi, I am trying to calculate the distance between two atoms, which are defined in an index file. The command that I use is: "gmx distance -f output.gro -s prod.tpr -n index.ndx -oav distance.xvg" I get the obvious: "Selection 'atom_name' does not evaluate into an even number of positions

Re: [gmx-users] Regarding Unknown cmap torsion between atoms

Hi, If your procedure for the two systems was actually the same, then the error does not come from your solute. Unfortunately only you know what is on line 8231... Work out what you did differently, e.g. by doing it again and making sure you do it the same way. Mark On Mon, Aug 21, 2017 at 7:27

Re: [gmx-users] Regarding Unknown cmap torsion between atoms

1] I created Diglycine peptide from chimera software, and got the .pdb file, added two different solvents (A, B) and made two different systems say, A-(Diglycine+solvent1), B-(Diglycine+solvent2). I generated the topology file from charmm36 FF by gmx pdb2gmx process for both the systems A and B

Re: [gmx-users] FEP calculations on multiple nodes

Hi, Where and What is the error? It is better to upload the file somewhere and providing a link here. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Regarding Unknown cmap torsion between atoms

Hi, On Mon, Aug 21, 2017 at 6:33 PM Dilip H N wrote: > Hello, > I have created a peptide from chimera software and got the pdb file, and i > have added solvents to it the resultant is mixture.gro, and used gmx > pdb2gmx to generate the topology using charmm36 FF. I

[gmx-users] Regarding Unknown cmap torsion between atoms

Hello, I have created a peptide from chimera software and got the pdb file, and i have added solvents to it the resultant is mixture.gro, and used gmx pdb2gmx to generate the topology using charmm36 FF. I got the topology correct, but nw if i give the command for energy minimization :- gmx grompp

Re: [gmx-users] FEP calculations on multiple nodes

Hi Micheal, ** What does the logfile say that was output?* *Ans : Log file output while running on PC (with command gmx mdrun -deffnm md_0 -nt 36 ). :* Using GPU 8x8 non-bonded kernels Removing pbc first time Pinning threads with an auto-selected logical core stride of 1 Initializing

Re: [gmx-users] FEP calculations on multiple nodes

Significantly more information is be needed to understand what happened. * What does the logfile say that was output? * What command are you using to run on multiple nodes? * What is the .mdp file? * How many nodes are you running on? * What version of the program? And so forth. On Mon, Aug 21,

Re: [gmx-users] Residue 1 mapping problem?

On 8/21/17 6:20 AM, morpheus wrote: Hi, I would like to simulate chain D and E of pdb-id 1oga but pdb2gmx complains about the first (?) residues of the 2 chains: "WARNING: WARNING: Residue 1 named GLN of a molecule in the input file was mapped to an entry in the topology database, but the

Re: [gmx-users] Error in simulated annealing

On 8/21/17 2:42 AM, Seera Suryanarayana wrote: Dear gromacs users, I wanted to do simulated annealing and I set up the .mdp file as follow... title = OPLS 4qam MD simulation define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md

Re: [gmx-users] Average and bfactors.pdb

On 8/20/17 11:48 PM, farial tavakoli wrote: blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear justin Thank you for your replyIt means, there is no problem, i can ignore

[gmx-users] Fwd: Question on gmx_wham with two reaction coordinates.

Hi all Sorry to post this again. I will appreciate if anybody can help with this I have a question on dealing with two reaction coordinates by gmx_wham. I did umbrella sampling on glucose 6-phosphate molecule on a poly-Lys peptide surface. Because the peptide is neither cylindrical nor spherical

Re: [gmx-users] MPICH2 error

Okay, it worked. After I put on -DCMAKE_C_COMPILER and -DCMAKE_CXX_COMPILER in my configuration options. Thanks. Souparno Adhikary, CHPC Lab, Department of Microbiology, University of Calcutta. On Mon, Aug 21, 2017 at 5:04 PM, Mark Abraham wrote: > Hi, > > Your

Re: [gmx-users] MPICH2 error

Hi, Your previous report didn't use eg CMAKE_CXX_COMPILER=mpic++ etc This should set up the linking. Anyway, if you build the shared version and don't build the static version of mpich nothing can go wrong. But there's nothing for gromacs to do about it... Mark On Mon, 21 Aug 2017 13:10

Re: [gmx-users] MPICH2 error

I am using MPI compilers to do the thing. I reinstalled MPICH2 using the options and it looks the same. Sorry... Souparno Adhikary, CHPC Lab, Department of Microbiology, University of Calcutta. On Mon, Aug 21, 2017 at 4:08 PM, Mark Abraham wrote: > Hi, > > Please use

[gmx-users] FEP calculations on multiple nodes

Hi everyone, I am trying runa FEP calculation with a system of ~25 particles. I have 20 windows and I am currently running my simulations on 1 node each. Since, my system is big, I just get 2.5ns in day. So, I thought to run each of my window on multiple nodes but for some reason, it crashes

Re: [gmx-users] MPICH2 error

Hi, Please use the MPI wrapper compilers provided by the MPI library to compile programs that use that MPI library, as I suggested last time. Managing this stuff is its job. Mark On Mon, Aug 21, 2017 at 12:34 PM Souparno Adhikary wrote: > I am posting this error again.

[gmx-users] MPICH2 error

I am posting this error again. Please help. I installed mpich2 with CXXFLAGS='-fPIC' and --enable-shared options. I configured gromacs with the following command: /root/cmake-3.9.1-Linux-x86_64/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON

[gmx-users] Residue 1 mapping problem?

Hi, I would like to simulate chain D and E of pdb-id 1oga but pdb2gmx complains about the first (?) residues of the 2 chains: "WARNING: WARNING: Residue 1 named GLN of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type

[gmx-users] Error in simulated annealing

Dear gromacs users, I wanted to do simulated annealing and I set up the .mdp file as follow... title = OPLS 4qam MD simulation define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps =

Re: [gmx-users] Pressure coupling incorrect number of values (I need exactly 2)-US simulation

Thank you very much, It worked with NVT, but the water molecule is not going though the channel at 0.01 nm per ns but It worked when i increased the pull_coord1_rate to 0.5 nm per ns from 0.01nm per ns but could not get proper histogram and energy profile. What parameters i need to change in