Re: [gmx-users] gromacs cpu v/s gpu

2014-01-15 Thread Tsjerk Wassenaar
Hi Gurunath, You have to run both simulations for (approximately) infinite time and compare the probability density functions to check whether the simulations are the same. Maybe running more simulations would also be a good idea. Here's something about simulations and statistics:

[gmx-users] PMF_Association

2014-01-15 Thread parisa amani
Dear All, I'm trying to examine the association of amino acid (gamma amino butric acid) in a non-polar solvent (trifluoroethanol). I calculated the PMF for three different concentrations of amino acid in solution along the distances between GABA molecules. Despite the fact that, increasing

Re: [gmx-users] non-native contatcs

2014-01-15 Thread bipin singh
First define and calculate the native contacts (contacts which were present in native reference structure and exist for significant amount of time during simulation). Then you can identify the contacts which exist for significant amount of time but were not present in native reference structure

Re: [gmx-users] LR electrostatics in single point energy calculations

2014-01-15 Thread Justin Lemkul
On 1/15/14, 7:14 AM, rajat desikan wrote: Hi All, I was wondering about the long range electrostatics while calculating single point energies. I did a cursory calculation for a protein in water (PME) and found that the LR electrostatic terms were zero. I know that the per-particle

[gmx-users] g_order (warning)

2014-01-15 Thread shahab shariati
Hi all I have DOPC lipid in my system. After preparing index file exactly based on how-to on the g_order page, I used following command to obtain order parameters of acyl chains: g_order -s md.tpr -f final.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o order_sn1.xvg I encountered following warnings:

[gmx-users] pdb2gmx

2014-01-15 Thread jwillcox
Hello, I was under the impression that pdb2gmx was supposed to referance the force fields as defined in oplsaa.ff/forcefield.itp, but it doesn't seem to be for me. To double check, I removed all force field parameters from forcefield.itp and pdb2gmx still ran and got the same result as before.

[gmx-users] -norandom option removed?

2014-01-15 Thread Albert
Hello: I found that the -norandom option in genion was no longer in 4.6.5: genion -h Option Filename Type Description -s topol.tpr InputRun input file: tpr tpb tpa -n index.ndx Input, Opt. Index

Re: [gmx-users] LR electrostatics in single point energy calculations

2014-01-15 Thread rajat desikan
Hi Justin, I used the following commands: mdrun_mpi -s md_6_50ns.tpr -rerun md_6_50ns.gro gmxdump_mpi -e ener.edr ener_readme And in the dump of the ener_readme file, I have the following terms: Coul-SR:Protein-Protein -6.62324e+05 LJ-SR:Protein-Protein -5.64854e+04 Coul-14:Protein-Protein

Re: [gmx-users] g_order (warning)

2014-01-15 Thread Justin Lemkul
On 1/15/14, 9:30 AM, shahab shariati wrote: Hi all I have DOPC lipid in my system. After preparing index file exactly based on how-to on the g_order page, I used following command to obtain order parameters of acyl chains: g_order -s md.tpr -f final.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o

Re: [gmx-users] -norandom option removed?

2014-01-15 Thread Justin Lemkul
On 1/15/14, 10:52 AM, Albert wrote: Hello: I found that the -norandom option in genion was no longer in 4.6.5: genion -h Option Filename Type Description -s topol.tpr InputRun input file: tpr tpb tpa

Re: [gmx-users] non-native contatcs

2014-01-15 Thread rajat desikan
Hi, I have never done this before. But is this a possibility? http://www.pymolwiki.org/index.php/Contact_map_visualizer On Wed, Jan 15, 2014 at 8:41 PM, bipin singh bipinel...@gmail.com wrote: Hello Dr. Justin, Yes, there is no in-built module in Gromacs to get the information about native

[gmx-users] scale tabulated non-bonded potentials?

2014-01-15 Thread Steven Neumann
Dear Gmx Users, Is there any way in Gromacs to scale tabulated potentials from energygrp_table (non-bonded)? Steven -- 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

[gmx-users] trouble with gaia....

2014-01-15 Thread Marc Hömberger
Hey Fra, if you have a few minutes could you maybe help me with some trouble I have with gaia? (session login seems to be corrupt / firefox cannot be started since it thinks I am still logged in seomwhere else) Best, Marc -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] trouble with gaia....

2014-01-15 Thread Marc Hömberger
I am sorry this email was send to the wrong list. please disregard. Best, Marc Hoemberger On Wed, Jan 15, 2014 at 5:01 PM, Marc Hömberger hoe...@gmail.com wrote: Hey Fra, if you have a few minutes could you maybe help me with some trouble I have with gaia? (session login seems to be

Re: [gmx-users] scale tabulated non-bonded potentials?

2014-01-15 Thread Mark Abraham
Yes, they get multiplied by parameters like charge, C6, C12 etc. Is that the question you're asking? :-) Mark On Wed, Jan 15, 2014 at 8:02 PM, Steven Neumann s.neuman...@gmail.comwrote: Dear Gmx Users, Is there any way in Gromacs to scale tabulated potentials from energygrp_table

Re: [gmx-users] LR electrostatics in single point energy calculations

2014-01-15 Thread Justin Lemkul
On 1/15/14, 4:18 PM, rajat desikan wrote: Hi Justin, Thanks for the reply. So, must I use a separate .mdp file with infinite cutoffs for both vdw and coulomb to get all the LR interactions correctly? Can you give me specific pointers about the settings? Infinite cutoffs, zero steps, don't

[gmx-users] About Tutorials

2014-01-15 Thread vidhya sankar
Dear Justin Thank you For your previous reply   I would like to do REMD (Replica exchange MD) in gromacs I am very happy if you paste  tutorial for REMD, Targeted MD , Constraint MD  and Non Equilibrium MD   as

Re: [gmx-users] About Tutorials

2014-01-15 Thread bharat gupta
Dear Vidya sankar, I think this may help you with the REMD. Here's the link for the tutorial: http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3a_Mark_Abraham%2c_Session_1B This tutorial deals with REMD and

[gmx-users] gromacs bond restraints

2014-01-15 Thread Neha Gandhi
How can I impose restraints in gromacs .mdp file or topology file to avoid isomerization of the peptide bond at the highest temperatures? Your help is appreciated -- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia

Re: [gmx-users] g_helix segmentation fault grom-4.6.5

2014-01-15 Thread Mark Abraham
Software has bugs, unfortunately, and GROMACS tools particularly so. We are trying to improve the situation, but if a developer isn't using a tool, it doesn't get any love! Are you trying to say it doesn't work in 4.6.5? Mark On Jan 16, 2014 5:51 AM, tarak karmakar tarak20...@gmail.com wrote:

Re: [gmx-users] gromacs bond restraints

2014-01-15 Thread Mark Abraham
See chapter four for what is available, and tables in 5.5 for a summary of their use. Mark On Jan 16, 2014 5:11 AM, Neha Gandhi n.gandh...@gmail.com wrote: How can I impose restraints in gromacs .mdp file or topology file to avoid isomerization of the peptide bond at the highest temperatures?