Yang Ye wrote:
Writing on local or remote certainly makes a difference. How about the
speed with no output at all?
Absolutely. Depending on the cluster setup, the best option is often
along the lines of
1) Write to disk physically associated with the CPUs (IIRC for GROMACS,
preferably the d
Writing on local or remote certainly makes a difference. How about the speed
with no output at all?
Regards,
Yang Ye
From: xianghong qi <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Sunday, November 9, 2008 12:36:40 AM
Subject: Re: [gmx-use
I'd like to know if the GMX_MAXCONSTWARN variable only turn off lincs warnings
or turn off the lincs algorithm fully? And how I do define this variable; I
imagine something like it at bashrc:
export GMX_MAXCONSTWARN=$GMX_MAXCONSTWARN:-1
is it correct?
Is there similar variable turns off p-coupli
shahrbanoo karbalaee wrote:
Dear justin
hi,
I minimized my peptides with gromacs 3,3,3 .Can I use this files
(em.gro) for pr and md with gromacs 3,3,1.?
Maybe, but it always best to keep consistent with the same version of Gromacs.
Version 3.3.3 introduces some bug fixes over 3.3.1, a
Dear justin
hi,
I minimized my peptides with gromacs 3,3,3 .Can I use this files
(em.gro) for pr and md with gromacs 3,3,1.?
best
--
sh-karbalaee
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The time difference is : for simulation with every 100ps output, 160ns/day;
for simulation with every 0.1ps output, It has been running for 4 days, only
wrote to 2300ps . I am not sure the local hard disk since I run my
simulation in some cluster. Thanks.
-Xianghong Qi
On Sat, Nov 8, 2008 at 11
thanks lot for your reply. My high frequency is every 0.1ps, low frequency
is every 100ps. I am not sure whether every 0.1ps is extremly high or not. I
am running with Gromacs 4.0. Up to now, I can see the only difference is the
speed between high frequency simulation and low frequency simulation.
More details please.
Local hard disk?
How much the time difference?
YY
On 11/8/08 12:41 PM, xianghong qi wrote:
Hello, all:
I compare the two simulations with different output frequency for .xtc
file in same machine. One with low frequency runs much faster than
the one with high frequency.
HI Chris
I followed the steps below and when i tried to run g_spatial it executed
g_cluster instead. Even when i do g_spatial -h it looks like its being
overwritten by g_cluster
1.I used make_ndx to create a group containing the atoms around which i want
the SDF
2. trjconv -s md.tpr -f tyrc_
Tsjerk Wassenaar wrote:
Hi,
Yes. You can use GROMACS to simulate traffic if you want to. :-)
Mark, do you have a force field for that?
Nah, parameterization against experimental data is really expensive.
Mark
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Hi,
> Yes. You can use GROMACS to simulate traffic if you want to. :-)
Mark, do you have a force field for that?
>> As i had done it with 4 residue with blocking group. But then i got the
>> error for rvdw and rlist as they should be nearer to cutoff value.
>> So instead of decreasing the value
On Sat, 2008-11-08 at 16:13 +1100, Mark Abraham wrote:
> xianghong qi wrote:
> > Hello, all:
> >
> > I compare the two simulations with different output frequency for .xtc
> > file in same machine. One with low frequency runs much faster than the
> > one with high frequency.
> > Is that reaso
Hi Tania,
The boolean options to the gromacs programs are (usually) set using
(e.g.) -mw | -nomw
Cheers,
Tsjerk
On Sat, Nov 8, 2008 at 5:00 AM, Mark Abraham <[EMAIL PROTECTED]> wrote:
> Tatsiana Kirys wrote:
>>
>> Hi,
>>
>> i got strange results using g_rms.
>> Does it by default uses mass wei
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