[gmx-users] Help with modified gmx_covar

Dear Gmx users, I need to ask you about a doubt I have regarding changing an analysis tool in Gromacs. More specifically g_covar. I found the modified source code for gmx_covar.c [ gmx_covar.c ] and I would like to replace the current

[gmx-users] Case sensitivity in atomtypes

Hello GMX users, I have some troubles with overriding parameters. I have generated parameters for lipids using Lipid11 forcefield for AMBER, based on GAFF, and Acpype. This forcefield contains atomtypes cA, cB for instance. When I include the bonded parameters in [bondtypes], [angletypes] sections

Re: [gmx-users] Running gmx-4.6.x over multiple homogeneous nodes with GPU acceleration

Thank you very much for both contributions. I will conduct some tests to assess which approach works best for my system. Much appreciated, Best regards, João Henriques On Tue, Jun 4, 2013 at 6:30 PM, Szilárd Páll wrote: > mdrun is not blind, just the current design does report the hardware > o

[gmx-users] Quartic angle potential - how to use?

Dear Gmx Users, I wish to use quartic angle potential and specify all constants. I know it is a function 6 of [ angles ] but do not know how to place my polynomial constants? Thank you, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-user

Re: [gmx-users] Running gmx-4.6.x over multiple homogeneous nodes with GPU acceleration

Sorry to keep bugging you guys, but even after considering all you suggested and reading the bugzilla thread Mark pointed out, I'm still unable to make the simulation run over multiple nodes. *Here is a template of a simple submission over 2 nodes:* --- START --- #!/bin/sh # # - - - - - - - - - -

[gmx-users] Re: how to add sodium acetate

Hi, Justin It's work ! Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/how-to-add-sodium-acetate-tp5008786p5008831.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] High Initial generated Temp

One more query Justin. Even if I don't use any sort of constraints in the final run, I'm not getting the initial temperature as exactly 300 K. Initial part of the .log file is as follows Initial temperature: 297.694 K Started mdrun on node 0 Wed Jun 5 16:58:40 2013 Step Ti

Re: [gmx-users] Running gmx-4.6.x over multiple homogeneous nodes with GPU acceleration

On Wed, Jun 5, 2013 at 2:53 PM, João Henriques < joao.henriques.32...@gmail.com> wrote: > Sorry to keep bugging you guys, but even after considering all you > suggested and reading the bugzilla thread Mark pointed out, I'm still > unable to make the simulation run over multiple nodes. > *Here is a

Re: [gmx-users] Help with modified gmx_covar

You need to call the newly compiled code. Either install the new version and source GMXRC appropriately, or use a full path to the new version in the build tree. Mark On Wed, Jun 5, 2013 at 11:05 AM, rohitarora wrote: > Dear Gmx users, > > I need to ask you about a doubt I have regarding chang

Re: [gmx-users] High Initial generated Temp

On Wed, Jun 5, 2013 at 3:06 PM, tarak karmakar wrote: > One more query Justin. > Even if I don't use any sort of constraints in the final run, I'm not > getting the initial temperature as exactly 300 K. Initial part of the .log > file is as follows > > > Initial temperature: 297.694 K > > Started

Re: [gmx-users] Running gmx-4.6.x over multiple homogeneous nodes with GPU acceleration

Ok, thanks once again. I will do my best to overcome this issue. Best regards, João Henriques On Wed, Jun 5, 2013 at 3:33 PM, Mark Abraham wrote: > On Wed, Jun 5, 2013 at 2:53 PM, João Henriques < > joao.henriques.32...@gmail.com> wrote: > > > Sorry to keep bugging you guys, but even after cons

Re: [gmx-users] Running gmx-4.6.x over multiple homogeneous nodes with GPU acceleration

Just to wrap up this thread, it does work when the mpirun is properly configured. I knew it had to be my fault :) Something like this works like a charm: mpirun -npernode 2 mdrun_mpi -ntomp 8 -gpu_id 01 -deffnm md -v Thank you Mark and Szilárd for your invaluable expertise. Best regards, João He

[gmx-users] Unknown bond_atomtype C2

Hello, I am getting "Unknown bond_atomtype C2" error for grompp. I don't have C2 atom in my .itp file. Here I used the .itp file ; For parameters see J. Phys. Chem. A. 2002, 106, 1074-1080 ; Derived from parsing of runfiles/alat.top.orig ;[ defaults ] ; nbfunccomb-rule gen-pairs

Re: [gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field

> It should also be noted (and obvious now that I actually look into it) that > using dispersion correction results in both the latent heat of vapourisation > and density of the alkanes being over estimated (for both Cut-off and > Reaction Field, and by the same amount). That may not be quite t

Re: [gmx-users] About coulmb & Vanderrwalls cutoff

On 6/4/13 10:13 PM, vidhya sankar wrote: Dear Justin thank you for your previous reply How can i check using th value 1.4 is harmless to My system Through g_energy ouput (potential.xvg) can i check (graphically) This is a topic that is a bit too hard to deal with via e

Re: [gmx-users] restraints on water oxygen atoms

On 6/4/13 11:47 PM, Shima Arasteh wrote: Dear gmx users, I have a POPC/peptide/water/ions system. I ran NVT and then NPT on my system. I'd prefer to run the equilibrium steps with position restraints on water oxygen atoms, because the water molecules penetrate the lipid bilayer when running

Re: [gmx-users] Quartic angle potential - how to use?

On 6/5/13 8:40 AM, Steven Neumann wrote: Dear Gmx Users, I wish to use quartic angle potential and specify all constants. I know it is a function 6 of [ angles ] but do not know how to place my polynomial constants? As table 5.5 in the manual indicates, list the equilibrium angle followed b

[gmx-users] diherdal psi vs angle teta plot

Dear Gmx Users, I wish to obtain the 2D scatter plot in which I will have my protein Ca-Ca-Ca tetta angle and the psi angle N(i)-CA(i)-C(k)-N(i+1) of the central residue? Would you please help? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

Re: [gmx-users] diherdal psi vs angle teta plot

On 6/5/13 2:13 PM, Steven Neumann wrote: Dear Gmx Users, I wish to obtain the 2D scatter plot in which I will have my protein Ca-Ca-Ca tetta angle and the psi angle N(i)-CA(i)-C(k)-N(i+1) of the central residue? Would you please help? Use g_angle to extract whatever quantities you want, th

[gmx-users] Snapshot and co-ordinate query

Hi, I have two questions. I have performed a simulation on my protein structure and after the simulation, I used trjconv to obtain snapshots after every 10 ns with the following command: trjconv -f md.xtc -s md.tpr -b 1 -e 10001 -o md_10.pdb and chose 0 (system) for the group. However, when

[gmx-users] (no subject)

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Re: [gmx-users] Snapshot and co-ordinate query

On 6/5/13 3:03 PM, Ankita naithani wrote: Hi, I have two questions. I have performed a simulation on my protein structure and after the simulation, I used trjconv to obtain snapshots after every 10 ns with the following command: trjconv -f md.xtc -s md.tpr -b 1 -e 10001 -o md_10.pdb T

[gmx-users] velocity-verlet giving nans

Hi I first performed a simulation using leap-frog integrator, which went well and got the expected results. For post-processing I want velocities at full time step, but, as per my understanding, leap-frog computes and writes velocities at half-time step. Therefore, I just changed integrator from '