Alright, thanks!
Am 17.02.2015 13:48, schrieb Mark Abraham:
Hi,
The second call to mdrun will run 1 steps if it can. Whether that is a
continuation or not depends what checkpoint mdrun finds, etc.
gmx mdrun -h says
-nsteps Run this number of steps, overrides .mdp option
This is true,
Dear all, the full log file is too big.
However in the middle part of it, there are only informations about
the energies at each time. The first part is alrady posted.
So I post the final part of it:
-
Step Time
On Wed, Feb 18, 2015 at 5:57 PM, Carmen Di Giovanni cdigi...@unina.it wrote:
Dear all, the full log file is too big.
Use pastebin or similar services.
However in the middle part of it, there are only informations about the
energies at each time. The first part is alrady posted.
OK, so first
I've just noticed something serious. Why are you calculating energies
every step? Doing that makes the non-bonded force calculation on
average 25-30% slower than e.g. calculating energies every 100-th
step.
You may be able to get another 5% or so form your GPU, could you post
the output of
Hi,
I am trying to simulate a peripheral membrane protein in a heterogenous
lipid bilayer of DOPC and DOPG using charmm 36 force field in GROMACS. i
need mdp files for NPT, NVT, steep and MD to check whether the conditions i
am using to simulate my system are appropriate or not.
--
Regards,
Dear Justin, thank you for the reply. However, I would like to know if
there is any server which can generate parameters for heme to be used in
OPLS-aa? We have already tried in swissparam with failed results. Please
help.
On 18 February 2015 at 21:15, Justin Lemkul jalem...@vt.edu wrote:
On
Justin,
the problem is evident for all calculations.
This is the log file of a recent run:
Log file opened on Mon Dec 22 16:28:00 2014
Host: localhost.localdomain pid: 8378 rank ID: 0 number of ranks: 1
On 2/18/15 11:20 AM, Carmen Di Giovanni wrote:
Justin,
the problem is evident for all calculations.
This is the log file of a recent run:
Again, this is *part* of a .log file, but at least we're starting to get
somewhere. Please realize that I'm not insisting on this for no reason; there
Dear all, I am trying to simulate a heme containing protein in high
concentration (having hydrogen peroxide). However, I do not know which
forcefield to use. Heme has forcefield in gromos96 but not the forcefield
of H2O2? Will generating .itp files for H2O2 from swissparam work? Please
help.
On 2/17/15 12:31 PM, Jin Zhang wrote:
Dear all,
We're doing free energy calculation and found some of my lambda job crashes
due to the combination of position restraint +refcoord_scaling COM. All
crashes happened at NPT steps.
By checking each energy term, we found the Position Rest. term is
On 2/17/15 5:14 PM, Udaya Dahal wrote:
Thanks Justin for prompt reply. Actually I calculated for the h_bonds with
same criteria for (angle 30 and distance(D-A) 0.35nm) from VMD, and the
number is lot less for both Polymer water and water water. I have 193
water molecules and the H-bond from
I post the message of a md run :
Force evaluation time GPU/CPU: 40.974 ms/24.437 ms = 1.677
For optimal performance this ratio should be close to 1!
NOTE: The GPU has 20% more load than the CPU. This imbalance causes
performance loss, consider using a shorter cut-off and a finer PME
What's your exact command?
Have you reviewed this page:
http://www.gromacs.org/Documentation/Acceleration_and_parallelization
James Wes Barnett
Ph.D. Candidate
Chemical and Biomolecular Engineering
Tulane University
Boggs Center for Energy and Biotechnology, Room 341-B
On 2/18/15 11:09 AM, Barnett, James W wrote:
What's your exact command?
A full .log file would be even better; it would tell us everything we need to
know :)
-Justin
Have you reviewed this page:
http://www.gromacs.org/Documentation/Acceleration_and_parallelization
James Wes Barnett
Dear James, this is the command:
gmx_mpi mdrun -s prod_30ns.tpr -deffnm prod_30ns -gpu_id 0
where gpu_id = 0 is INVIDIA Tesla K20
--
Carmen Di Giovanni, PhD
Dept. of Pharmaceutical and Toxicological Chemistry
Drug Discovery Lab
University of Naples Federico II
Via D. Montesano, 49
80131
Daear all,
I'm working on a machine with an INVIDIA Teska K20.
After a minimization on a protein of 1925 atoms this is the mesage:
Force evaluation time GPU/CPU: 2.923 ms/116.774 ms = 0.025
For optimal performance this ratio should be close to 1!
NOTE: The GPU has 25% less load than the CPU.
On 2/18/15 9:18 AM, Sanchaita Rajkhowa wrote:
Dear all, I am trying to simulate a heme containing protein in high
concentration (having hydrogen peroxide). However, I do not know which
forcefield to use. Heme has forcefield in gromos96 but not the forcefield
of H2O2? Will generating .itp files
On 2/18/15 10:30 AM, Carmen Di Giovanni wrote:
Daear all,
I'm working on a machine with an INVIDIA Teska K20.
After a minimization on a protein of 1925 atoms this is the mesage:
Force evaluation time GPU/CPU: 2.923 ms/116.774 ms = 0.025
For optimal performance this ratio should be close to 1!
We need a *full* log file, not parts of it!
You can try running with -ntomp 16 -pin on - it may be a bit faster
not not use HyperThreading.
--
Szilárd
On Wed, Feb 18, 2015 at 5:20 PM, Carmen Di Giovanni cdigi...@unina.it wrote:
Justin,
the problem is evident for all calculations.
This is the
Dear Justin,
We thought about this, and checked these non-crashed lambda tpr as well as
the pre-equilbrated NPT step, all showed mismatch between posre-com[0]
posre-com[1] posre-com[2], and the real com. So I suspect this posre-com is
not the real center of mass for NPT simulation.
Since the
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