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 reference coordinate is read from -c .gro when perform grompp, it
should not be wrong, unless it read elsewhere.
Best,
Jin
Date: Wed, 18 Feb 2015 07:42:30 -0500
From: Justin Lemkul jalem...@vt.edu
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] free energy calculation: combination of
position restraint +refcoord_scaling cause crash during NPT
Message-ID: 54e488b6.9090...@vt.edu
Content-Type: text/plain; charset=windows-1252; format=flowed
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
surprisingly as high as 10^6 kJ/mol, the others look fine. Either turn of
position restrain or refcoord_scaling could avoid the simulation to be
crashed. We tried to see if there's mismatch of either COM or coordinate
and found no direct answer.
Any help would be appreciated!
In the tpr file
refcoord-scaling = COM
posres-com (3):
posres-com[0]= 3.15034e-01
posres-com[1]= 4.48110e-01
posres-com[2]= 5.17730e-01
COM of protein-ligand calculated by t_traj -com -ox
3.024224.301694.84964
If the reference COM is defined as (0.315,0.448,0.518) and your actual
coordinates are what you're shown above, there will inherently be a huge
restraint potential as mdrun tries to bias the coordinates towards the
defined
reference. I suspect something is wrong in your definition of your
reference.
-Justin
coordinate of 1st atom in tpr: posres_xA[0]={ 1.39783e-01,
-9.56922e-02, 1.22536e+00}
coordinate of 1st atom in gro: 1MOL C11 3.164 4.206
6.075
The same thing was also found in a normal non-free energy simulations
with
combination of position restrain and refcoord-scaling.
Later on, we found some other people also have the same problem when use
that combination to do free energy calculation.
http://comments.gmane.org/gmane.science.biology.gromacs.user/66177
It makes more sense to me to turn on refcoord_scaling while using
position
restraint.
Again, any help to understand this would be appreciated!
Regards,
Jin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
--
Message: 3
Date: Wed, 18 Feb 2015 19:48:50 +0530
From: Sanchaita Rajkhowa srajkhow...@gmail.com
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] simulation of heme along with h2o2
Message-ID:
CACE5zdsaXX==in=SPntZiaRZ=+
nrjnyajn8uwmmwysvsr4x...@mail.gmail.com
Content-Type: text/plain; charset=UTF-8
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.
Thanks in advance.
Sanchaita.
--
Message: 4
Date: Wed, 18 Feb 2015 16:30:34 +0100
From: Carmen Di Giovanni cdigi...@unina.it
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] GPU low performance
Message-ID: 8525B4BE52BB4609BCED7556FAFB3587@PCCarmen
Content-Type: text/plain; charset=iso-8859-1
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. This imbalance causes
performance loss.
Core t (s) Wall t (s) (%)
Time: 3289.010 205.891 1597.4
(steps/hour)
Performance: 8480.2
Finished mdrun on rank 0 Wed Feb 18 15:50:06 2015
Cai I improve the performance?
At the moment in the forum I didn't full informations to solve this
problem.
In attachment there is the log. file
thank you in advance
Carmen Di Giovanni
--
Carmen Di Giovanni, PhD
Dept. of Pharmaceutical and Toxicological Chemistry
Drug Discovery Lab
University of Naples Federico II
Via D. Montesano, 49
80131 Naples
Tel.: ++39 081 678623
Fax: ++39 081