Re: [gmx-users] cluster analysis_group selection
Hi, Hope this helps: https://ctlee.github.io/BioChemCoRe-2018/clustering/ In case you may want to align the trajectory using one group but calculate RMSD using another group, you can choose no fit when doing clustering. In that case, gmx trajconv can be used before doing clustering. Best, Jin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] nvt equilibration
Hi Marzieh, the group name may be Water_CL since you selected 4 | 9, but check your index.ndx to make sure. Regards, Jin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] free energy calculation: combination of position restraint +refcoord_scaling cause crash during NPT (Justin Lemkul)
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
[gmx-users] free energy calculation: combination of position restraint +refcoord_scaling cause crash during NPT
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
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
--
Gromacs Users mailing list
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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[gmx-users] [ pairs_nb ] in topology
Dear all, Does anyone know how to write [ pairs_nb ] in topology? I read the Manual 4.6.5, only chapter 5.3.4 and Table 5.5 described the [ pairs_nb ]. Based on Table 5.5, I wrote like this: [ pairs_nb ] 1 2 1 -0.044600 -0.162400 3.39967e-01 3.59824e-01 But I got an error like this: case: 20 --- Program grompp, VERSION 4.6.5 Source code file: /gromacs/4.6.5/src/gromacs-4.6.5/src/gmxlib/gmx_fatal.c, line: 597 Fatal error: Invalid case in switch statement, file /gromacs/4.6.5/src/gromacs-4.6.5/src/kernel/topio.c, line 1007 Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Temperature of protein-ligand systems
Hi, I think it depends on the purpose of your simulation. If you want to simulate an in vivo environment, then you may use 310 K, for example. 2014-05-18 12:00 GMT+02:00 gromacs.org_gmx-users-requ...@maillist.sys.kth.se: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Temperature of protein-ligand systems (Jacob Babinec) -- Message: 1 Date: Sun, 18 May 2014 05:25:13 -0400 From: Jacob Babinec jsb...@drexel.edu To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Temperature of protein-ligand systems Message-ID: fcccd8bd5a60d.53784...@drexel.edu Content-Type: text/plain; charset=us-ascii Dear Gromacs users, I have been debating about what temperature I should use for my protein-ligand simulation. I have seen majority of people in the literature use 300 K; however, this confuses me because 310 K is body temperature. Can anybody lead me in the right direction? Thank you very much, Jacob Babinec -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. End of gromacs.org_gmx-users Digest, Vol 121, Issue 82 ** -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
