Re: [gmx-users] Updating GTX670 PCIE speed from 5GT/s to 8GT/s resulted in about 10% speedup of md_run.

2013-12-04 Thread Szilárd Páll
Hi Henk, Thanks for the useful comments! When you run on a single GPU, you do get full timing details both on CPU and GPU - just have a look at the performance tables at the end of the log file. Alternatively you can simply run nvrpof mdrun which will by default give you a nice overview of

Re: [gmx-users] heating

2013-12-04 Thread rajat desikan
Hi Kiana, I always heat from 5 K to 300 K with ref_t=300 (ending temp) and gen_temp=5 (starting temp). 5 K is as good as starting at 0 K for my systems. Hope that helps. Regards, On Wed, Dec 4, 2013 at 12:18 PM, kiana moghaddam ki_moghad...@yahoo.comwrote: Dear Jastin Thanks very much for

[gmx-users] How to make OPLS forcefield?

2013-12-04 Thread Pham Kim
Dear Gromacs User, I am the beginner using Gromacs. I have created polyethylene .gro and .top using http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg but in that .top, forcefield is gmx.ff/forcefield.itp. I want to simulate with OPLS forcefield. Please help me how to make or convert to OPLS ff.

[gmx-users] rcoulomb, rvdw and rlist value

2013-12-04 Thread kiana moghaddam
Dear Users I want to use parmbsc0 force field for DNA-ligand interaction. I want some information about value of rcoulomb, rvdw and rlist in mdp file during equilibration production steps. I set these values 1 nm . Is it correct? Best regards -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread panzu
Hello users, After downloading the toluene.pdb file of a toluene molecule and its forcefield tolu.itp from Automated Topology Builder and saved in the root /usr/share/gromacs/top/gromos53a6.ff I use the next comand i order to convert the pdb format to .gro :

Re: [gmx-users] out of disk space error

2013-12-04 Thread Justin Lemkul
On 12/4/13 5:24 AM, a...@imtech.res.in wrote: I think so. You are outputting the information too often i.e every 0.2 ps i.e. 5000 times per ns. See this thread http://comments.gmane.org/gmane.science.biology.gromacs.user/32721 It is unlikely that a few hundred ps of NVT would fill up

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread Justin Lemkul
On 12/4/13 6:15 AM, panzu wrote: Hello users, After downloading the toluene.pdb file of a toluene molecule and its forcefield tolu.itp from Automated Topology Builder and saved in the root /usr/share/gromacs/top/gromos53a6.ff I use the next comand i order to convert the pdb format to .gro :

Re: [gmx-users] GROMACS 4.6.5 is released

2013-12-04 Thread Szilárd Páll
On Wed, Dec 4, 2013 at 10:15 AM, João Henriques joao.henriques.32...@gmail.com wrote: Soon enough we will have daily releases :P I hope you're not suggesting that we should release less frequently! :) Mark, can you please elaborate just a tiny bit longer on how relevant were the GPU-load

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread panzu
so How do I convert from .pdb to .gro? -- View this message in context: http://gromacs.5086.x6.nabble.com/Atomistic-Simulation-tp5012984p5013059.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread Justin Lemkul
On 12/4/13 9:06 AM, panzu wrote: so How do I convert from .pdb to .gro the ? You don't technically need one: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File If you prefer to use .gro format, just convert with editconf. The job of pdb2gmx is to produce a topology; the

Re: [gmx-users] GROMACS 4.6.5 is released

2013-12-04 Thread João Henriques
I did read it and wasn't very enlightened by it, that's why I kindly requested for further information on the subject. under certain circumstances (but quite often), a segmentation fault occurs definitely sounds serious, but it's not very explicit. In any case, I'll request a new install and tell

Re: [gmx-users] flags for internal coordinates restraints

2013-12-04 Thread gromacs query
LINCS or SHAKE (all atoms) can be used for this? or some better options available? it can be seen as two protein helix interacting with each other as rigid bodies... thanks On Wed, Nov 27, 2013 at 12:35 AM, gromacs query gromacsqu...@gmail.comwrote: Dear All I want to simulate two polymer

Re: [gmx-users] atom name - topology

2013-12-04 Thread Justin Lemkul
On 12/4/13 11:48 AM, Steven Neumann wrote: Dear Gmx Users, My molecule contains 2516 atoms made of 5 type of beads: BAS, POL, NON, ACI, GLY and I want to create a topology. Is it possible to make one residue of one [ moleculetype ] with this number of atoms so that: [ moleculetype ] ; Name

Re: [gmx-users] force field for prodrg server

2013-12-04 Thread Mahboobeh Eslami
dear Justin thanks for reply I don't find tutorial for ATB and I don't know that which files are used for itp and gro files from ATB result, Moreover in gromacs site is mentioned  that PRODRG is used  for GROMOS96 force field, 43A1. can I use ATB for 43A1 force field? On Wednesday, December

Re: [gmx-users] out of disk space error

2013-12-04 Thread bipin singh
If none of the earlier suggestions worked then, it could be a simple problem of power port from which you have connected your hard disk. Try reconnecting the hard disk and and retry running the mdrun. Posting the exact commands used while writing the output during mdrun, may help to trace the

Re: [gmx-users] GROMACS 4.6.5 is released

2013-12-04 Thread Szilárd Páll
The first update on the redmine page does describe the source of the issue - although perhaps not in the most user-friendly manner. Translating it to a simple example, if you have dual-socket 8c nodes and 2 GPUs per node: mpirun -np 4 mdrun -ntomp 4 -gpu_id 0011 #single node 4 ranks per node,