Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

.3121 Pot 3084.9904 2993.2110 -91.7794 On Tue, Apr 30, 2013 at 8:33 PM, Justin Lemkul wrote: > > > On 4/30/13 4:19 PM, Reza Salari wrote: > >> Hi >> >> I have set up two small systems, one with a single POPC lipid, and another >> system with 23 POPC'

[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

r the single POPC, all the potential energy terms match very well, but for the membrane system the non-bonding terms differ significantly. I am providing the full details below and greatly appreciate any hint for better comparison of the energies. Thanks, Reza Salari Details: 1) Both systems

Re: [gmx-users] New ion parameters and OPLS-AA

different combination rules. If I there is no OPLS parameters based on LB rule, as you mentioned I have to switch to some ff like Amber. Regards, Reza Salari From: David van der Spoel To: Discussion list for GROMACS users Sent: Wed, December 16, 2009 1:08:58 PM S

Re: [gmx-users] New ion parameters and OPLS-AA

different approaches. Regards, Reza Salari From: Alexandre Suman de Araujo To: gmx-users@gromacs.org Sent: Wed, December 16, 2009 11:36:50 AM Subject: Re: [gmx-users] New ion parameters and OPLS-AA If you decide to change the ions parameters, you can use the

Re: [gmx-users] New ion parameters and OPLS-AA

compatible with the OPLS-AA combination rule. Although based on Horinek paper I was sort of hoping that I could convert the parameters for different combination rules. Regards, Reza Salari From: David van der Spoel To: Discussion list for GROMACS users Sent: Wed

Re: [gmx-users] New ion parameters and OPLS-AA

paper converted the sigma values for different combination rules. It seems that there must be a relatively direct way to do this without going through the re-parametrization process. Regards, Reza Salari From: Andrew Paluch To: Discussion list for GROMACS users

[gmx-users] New ion parameters and OPLS-AA

explanation but without luck. I really appreciate any help on clarifying this. Regards, Reza Salari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't po

Re: [gmx-users] Exclusions in topology file seem not working for big systems

so it seems that I don't need to use exclusions anymore. Regards, Reza Salari From: Berk Hess To: Discussion list for GROMACS users Sent: Fri, December 4, 2009 8:01:34 AM Subject: RE: [gmx-users] Exclusions in topology file seem not working for big sy

Re: [gmx-users] Exclusions in topology file seem not working for big systems

about is if I want to exclude all non-bonding interactions inside a small molecule, do I need to remove [pairs] when adding the [exclusions]? I am using OPLSAA. Regards, Reza Salari From: Berk Hess To: Discussion list for GROMACS users Sent: Thu, December 3

Re: [gmx-users] Exclusions in topology file seem not working for big systems

rested in dV/dl values, which in this case is related to the electrostatic interaction of a residue with water as the charges on that residue being turned off). Regards, Reza Salari From: Berk Hess To: Discussion list for GROMACS users Sent: Thu, December

Re: [gmx-users] Exclusions in topology file seem not working for big systems

. Regards, Reza Salari From: David van der Spoel To: Discussion list for GROMACS users Sent: Wed, December 2, 2009 11:59:49 AM Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems Reza Salari wrote: > Hi All, > > I seem

[gmx-users] Exclusions in topology file seem not working for big systems

n be defined in the exclusion section of topology file? I appreciate any hint or help. Regards, Reza Salari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don&

Re: [gmx-users] Different bonding energies for two almost the same systems

t for frozen test? Reza From: Mark Abraham To: Discussion list for GROMACS users Sent: Wed, November 4, 2009 11:37:32 AM Subject: Re: [gmx-users] Different bonding energies for two almost the same systems Reza Salari wrote: > Dear Gromacs Users, > > I

[gmx-users] Different bonding energies for two almost the same systems

test with steep algorithm and also md dyanmics but the energies are still different. Thank you in advance, Reza Salari 4_md_md.mdp Description: Binary data bound.pdb Description: Binary data out_bound.log Description: Binary data ubound.pdb Description: Bina

[gmx-users] Freezing Algorithm

Hi all, I've got a question regarding freezing algorithm in GROMACS. I appreciate it if somebody explains this. I think in GROMACS 3 for freeze option to work it was generally suggested that all the interactions inside the frozen part should be excluded (either in top or mdp files). However it se

[gmx-users] A Question About gmxtest

Hi everyone! Thanks to GROMACS developers, version 4.0.4 has been released along with gmxtest 4.0.4. However, I have encountered some problems in passing all tests. I have installed GROMACS on different machines (64 bit AMD and Intel quad cores) using diffrent configure flags (based on instruct

Re: [gmx-users] Domain Decomposision and Frozen Groups

roups to work. Any help or hint is highly appreciated! Reza Salari Express yourself instantly with MSN Messenger! MSN Messenger Express yourself instantly with MSN Messenger! MSN Mess

Re: [gmx-users] Domain Decomposision and Frozen Groups

, but without any success. Can you please point out where is the source of this error and how I can get domain decomposition and frozen (or restraint) groups to work. Any help or hint is highly appreciated! Reza Salari Express yourself instantly

[gmx-users] Domain Decomposision and Frozen Groups

help or hint is highly appreciated! Reza Salari ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't pos

Re: [gmx-users] Freezing Groups

is it more convenient and much more efficient to use energy monitor group exclusions". The "much more efficient" part concerns me a little bit. Because I am looking for efficiency, can you give me an idea about how using energygrp_excl is more efficient than using [exclusions]?

[gmx-users] Freezing Groups

erent ligands), don't those "unexcluded coulomb energies" cancel out each other when comparing the total energies of the two states? Or there is no guarantee for this? Thank you in advance. Any kind of help is really appreciated. Reza Salari

[gmx-users] GromacsGUI 0.5.2 is available.

by giving your feedback about bugs, problems and your suggestions. Sincerely, Reza Salari ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search