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
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
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.
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
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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 :
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
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 :
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
so How do I convert from .pdb to .gro?
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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
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
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
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
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
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
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,
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