Re: [gmx-users] gromacs 5 pdb2gmx does not faithfully reproduce the AMBER99sb-ILDN force field

Em 22/07/2015 14:51, Christopher Neale chris.ne...@alum.utoronto.ca escreveu: Dear Users: I believe that gromacs 5 pdb2gmx does not faithfully reproduce the AMBER99sb-ILDN force field. It is not exclusive behavior for any particular FF. I've got same error for Gromos54a7. If one uses multiple

Re: [gmx-users] gromacs 5 pdb2gmx does not faithfully reproduce the AMBER99sb-ILDN force field

Hi Chris and everyone, The bug in question affects 5.0.x and it is related to the hackblock handling of pdb2gmx. As the above linked redmine page indicates, it is indeed a duplicate of previously reported issues (#1755 and #1755). It has been first identified and fixed as a bug a few weeks ago,

Re: [gmx-users] Reverse micelle clustering issue

Thank you for your response! I used the code that you provided and my micelle is now in the middle. My mass ratio for isooctane is about 88% if you were still curious. Once again thank you for your help. Thank you, Tyler Cropley On Wed, Jul 22, 2015 at 4:57 AM, ABEL Stephane 175950

[gmx-users] Reverse micelle clustering issue

Hello To center your RM inside teh box you could use to successive trjconv commands with pbc cluster and mol in index.ndx 0 : all 1 AOT 2 water 3 AOT_Water 4 ISO 1 -- select 1 1 0 (or 2 2 0) echo 1 1 0 | trjconv -f my_initial.xtc -s my_tpr.tpr -pbc cluster -ur compact -center -o

[gmx-users] Fwd: itp file not found

Hi all, I am running energy minimization and grompp is complaining about following error. I am using Gromacs version 4.6.3. On Gromacs website it is saying that GROMOS96 54A7 files from ATB website were added to 4.6.2 and later versions right?

[gmx-users] itp file not found

Hi all, I am running energy minimization and grompp is complaining about following error. I am using Gromacs version 4.6.3. On Gromacs website it is saying that GROMOS96 54A7 files from ATB website were added to 4.6.2 and later versions right?

[gmx-users] Fwd: itp file not found

Hi all, Sorry apparently my previous emails the shared links just contained one file, apologize for that. I am running energy minimization and grompp is complaining about following error. I am using Gromacs version 4.6.3. On Gromacs website it is saying that GROMOS96 54A7 files from ATB website

Re: [gmx-users] g_msd and Diffusion Constant

If the error bar exceeds the absolute value of diffusion coefficient, just round the number, as I exemplified below. The error bar should correspond to the last digit of the result value, e.g. 5 +/ -2; 0.0002 +/- 0.0001; 0.4E6 +/- 0.2E6, etc. My immediate guess is that the problem in the code is

Re: [gmx-users] Distance issue

Hmm. If you exclude PBC manually, do you get a pick when expected? Professor Vitaly V. Chaban On Wed, Jul 22, 2015 at 8:10 AM, Navneet Chaturvedi 14.navn...@gmail.com wrote: Dear Scientists My system contains Protein+ZN+ions+water. Box size from protein surface is 1.0nm. After production

[gmx-users] (no subject)

How to select isovalue in spatial density distribution for solvation shell and bulk around the solute? -- *Mayank Kumar Dixit * Senior Research Fellow Molecular Dynamics lab Department of Chemistry IIT Bombay Powai, Mumbai. Mob No 9820697156 -- Gromacs Users mailing list * Please search the

Re: [gmx-users] angle between two vectors

Thanks a lot Teemu, i will try! Best regards, Natalia 2015-07-21 7:48 GMT-04:00 Teemu Murtola teemu.murt...@gmail.com: It's not clear from your question what you exactly want to calculate, but g_sgangle (Gromacs 4.6 and earlier) and gmx gangle (Gromacs 5.0+) can calculate angles between

Re: [gmx-users] GROMACS 5.0.5 GPU version on K620

Krzysztof, Thanks for getting back. I was interested in the -version output of the problematic binary hoping to pinpoint the source of the issues you reported - especially because that error should not have occurred to begin with (unless you changed compiler flags manually!). The poor

Re: [gmx-users] Create file topology in oplsaa

you can also look at this tutorial if you want to have starting point for generating topologies: http://www.esi.umontreal.ca/~pelletjo/gromacs/ max On Jul 21, 2015, at 9:52 AM, gozde ergin gozdeeer...@gmail.commailto:gozdeeer...@gmail.com wrote: Gromacs has OPLSAA force field. You can use

Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0

Dear Eudes: There are two issues: The first issue is the fact that you've got a sampling problem near the bilayer center. The second issue is the periodic bumps that you see in your PMFs. I'll take the second part first. The source of the periodic bumps in PMFs from umbrella sampling is, to