n GMX (and another work about it).
And are there bigger differences (if someone knows) in use 1 Gbps
onboard NIC vs. "better"? add-on NIC cards e.g. Intel Pro/1000 CT or
similar? In MPI calculations with use 4 to 8 cores per computing node.
Thanks a lot.
Milan Melichercik
--
gm
On Tuesday 20 April 2010 18:02:50 Bharath.K. Chakravarthi wrote:
> hi all
> I'm running simulation for a protein of about 150 amino acids for 100
> steps i.e 2 ns in a system of about 35 GB disk space.
> is there any way to know the approximate size of generating data.
>
The grompp c
On Friday 19 March 2010 02:36:49 Stefan Hoorman wrote:
> I have tried using g_bundle in order to analyse helix axes in my
> transmembran helices. I created two groups in my ndx file that included the
> alpha carbons of the first half of my helix and a second group for the
> alpha carbons for the s
supti mukherjee wrote:
Dear gromacs users,
I have some doubts regarding the options to be selected in g_sas
program. g_sas asks for two groups, first one for calculation and second
one for output. As I have understood from the manual that first group
should contain all non solvent groups and s
On Wednesday 17 March 2010 13:53:03 Carla Jamous wrote:
> Hi everyone,
>
> It's the first I use the process of extending simulations.
> I did the following:
> tpbconv -s prot.tpr -extend 6000 -o protein.tpr
>
> mdrun -v -s protein.tpr -cpi state.cpt -cpo state_a.cpt -o protein.trr -c
> protein.gr
On Wednesday 27 January 2010 19:40:57 Guilherme Menegon Giesel wrote:
> Hello folks!!
>
> Does anyone know if there is a GROMACS version to commercial use, or under
> somekind of license?
> If so, how should I proceed to get such license?
> Best regards!!
>
Gromacs is under GPLv2 license (http:/
Dňa Pi 16. Marec 2007 14:19 Triguero, Luciano O napísal:
> Dear Users,
>
> Thank for your help. I started a 10 ns simulation, but it dies because of
> an error in the cluster PBS system, so I want to continue the simulation
> from the last (r,v) point. May I still use tpbconv to restart from that
>
(and all of available CPU cores on it). I can't give
you more specific answer cause I don't know your cluster. But the best
result, I think, you can have simply by try the job on 1, 2, 3, etc. nodes...
Milan Melichercik
___
gmx-users mailin
Dňa Št 7. September 2006 15:27 Navratna Vajpai napísal:
> Dear All..
> to continue the run, as i understood, I modified the md.mdp and then
> use the .tpr and .trr for the further run. Can anyone suggest that it
> is the right way or not? actually in one of the tutorials note i have
> just found to
Hi guys,
maybe I ask stupid question and I missed something, but I want to compute
radial densities (perpendicular to an axis of a alpha helix peptide), but I
couldn't find suitable program to do this job.
Thanks a lot for help
Milan
___
gmx-users mail
Dňa St 23. August 2006 13:42 mahbubeh zarrabi napísal:
> dear itamar
> where is adress make-hole site?
> thanks
3rd record on following page
http://www.gromacs.org/contributed_by_users/task,cat_view/gid,24/dir,DESC/order,name/limit,5/limitstart,5/
___
gm
Dňa Ne 30. Júl 2006 01:47 zazeri napísal:
> The precision of Gromacs compiled for single precision
> on 64 bits machine is equal to precision of Gromacs
> compiled for double precision on 32 bits machine ?
AFAIK no. The single precision is 32bit floating point number, double is 64
bit - on ALL pl
Dňa Ut 18. Júl 2006 16:20 Diane Fournier napísal:
> Hi gromacs users
>
> I've already used gromacs single-processor version and I want to use the
> parallel version of gromacs on a SGI Altix 2700 with 32 processors. I'm
> wondering how to proceed, because this does not seem to be explained
> proper
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