Re: [gmx-users] NPT equilibration in KALP15-DPPC

 Hi, After the NPT mdrun, I visulized the npt.gro. I need to know if this npt.gro is the final result of equilibration? I see 2,3 water molecules between the lipid chains. Should I remove them? Can I remove them? Or it's not the step that I can make such a decision? Thanks in advance. Sincer

RE: [gmx-users] BAR / g_bar problems

Trivial question, how do the TI results compare? Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you

Re: Re: [gmx-users] User specified potential functions

Hi Mark I transfered all the table files with the dos2unix tool, and it worked. Thank you so much! Best regards! 2012-08-27 toby1024 Message: 2 Date: Mon, 27 Aug 2012 08:31:55 +1000 From: Mark Abraham Subject: Re: [gmx-users] User specified potential functions To: Discussion list for GROM

Re: [gmx-users] GROMACS command for energy calculation

On 8/26/12 7:44 PM, Acoot Brett wrote: Dear All, I am still confused and I hope I can get some detailed explaination. For example, I want to determine the interaction energy between residue 52 and residue 105, how should I set energyggryp and what is the related commands? And if I want to d

Re: [gmx-users] GROMACS command for energy calculation

Dear All,   I am still confused and I hope I can get some detailed explaination. For example, I want to determine the interaction energy between residue 52 and residue 105, how should I set energyggryp and what is the related commands?   And if I want to determine the interaction energy between r

Re: [gmx-users] Re: Cross-correlation maps

On 24/08/2012 4:51 PM, James Starlight wrote: up :) It's appeared two additional questions. 1) In addition to the pca's cross-correlation maps I wounder to know about possibility of calculation of such cross-correlation's from the trajectories indirectly without calculation of the covariance mat

Re: [gmx-users] CHARMM and FEP calculations

On 24/08/2012 11:28 PM, Wright, Louise wrote: Hi I asked a similar question a year ago about implementing CMAP in FEP calculations for gromacs 4.5.4. At the time I could not get the simulation to run with CMAP as it came up with: Fatal error: Function type CMAP Dih. not implemented in ip_pert

Re: [gmx-users] Topology- make bonds with certain cut-off distance

On 25/08/2012 11:58 PM, mohan maruthi sena wrote: Hi , Thanks for your reply. I actually want to build an elastic network model (ENM) for Protein containing 372 residues. According to literature, ENM model only considers C-alpha atoms of protein and discards rest of the atoms.The potential

Re: [gmx-users] User specified potential functions

On 25/08/2012 10:28 PM, toby1024 wrote: > Dear Uses: > I am using "User specified potential functions" with Gromacs-4.5.4. According > to the manual, I wrote a FORTRAN program to generate the table.xvg file. When > I ran mdrun, the error came out as below: > > .. > Only 7 columns on line

Re: [gmx-users] GROMACS command for energy calculation

On 27/08/2012 8:01 AM, Acoot Brett wrote: Dear Justin, In the internet there is the following content. But if I need to measure the non-bonded energy between residues within a protein, or between fragments within a protein, can you advise on how to set up the energygrp? http://www.gromacs.or

Re: [gmx-users] GROMACS command for energy calculation

On 8/26/12 6:01 PM, Acoot Brett wrote: Dear Justin, In the internet there is the following content. But if I need to measure the non-bonded energy between residues within a protein, or between fragments within a protein, can you advise on how to set up the energygrp? You can use whatever

Re: [gmx-users] GROMACS command for energy calculation

Dear Justin,   In the internet there is the following content. But if I need to measure the non-bonded energy between residues within a protein, or between fragments within a protein, can you advise on how to set up the energygrp?   Cheers,   Acoot  Energy group exclusions energygrp_excl: Pairs

Re: [gmx-users] GROMACS command for energy calculation

On 8/26/12 5:02 PM, Acoot Brett wrote: Dear All, After the production MD has been done, does GROMACS has a command which can calculate the interaction energy between any 2 residues in a frame of structure from the MD? Assuming you have made proper use of energygrps in the .mdp file, you c

[gmx-users] GROMACS command for energy calculation

Dear All,   After the production MD has been done, does GROMACS has a command which can calculate the interaction energy between any 2 residues in a frame of structure from the MD?   Cheers,   Acoot  -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

[gmx-users] Elastic network model -building

Hi all, I want to build elastic network model for a protein. To build an Elastic network model , I consider only C-alpha atoms of the protein. I want to make c-alpha atoms connect(make bond) with all the other c-alpha atoms , if it falls within certain cut-off distance. How can i do t

Re: [gmx-users] NPT equilibration in KALP15-DPPC

On 8/26/12 8:54 AM, Shima Arasteh wrote: Hi, For NPT equilibration of KALP15 in DPPC following the Justin's tutorial, when I run the grompp command, I get 4 notes. Is it necessary to pay attention to the notes ? Are they notable? Notes are generally notable, yes ;) Never ignore anything

[gmx-users] NPT equilibration in KALP15-DPPC

 Hi, For NPT equilibration of KALP15 in DPPC following the Justin's tutorial, when I run the grompp command, I get 4 notes. Is it necessary to pay attention to the notes ? Are they notable? NOTE 1 [file npt.mdp]:   You are using a cut-off for VdW interactions with NVE, for good energy   cons

Re: [gmx-users] Protein-POPC bilayer

Dear Dr.Dallas, Would you mind please sending the article as soon as it's printed? I would appreciate you. Thanks. Regards, Shima From: Dallas Warren To: Discussion list for GROMACS users Sent: Friday, August 17, 2012 7:30 AM Subject: RE: [gmx-users] Prote