Re: Re: [gmx-users] problem with protein secondary structure analysis

Hi Minnale, We do appreciate that english is not your native language (it isn't mine either), but please try to write correct, complete sentences. That will make it easier to read your posts, understand what you did and where you went wrong and how we can, maybe, provide you a solution. Justins r

[gmx-users] Out of office AutoReply

Out of office AutoReply => August the 31th For urgent matters, please contact Colette Zeches: [EMAIL PROTECTED] +32(0)81-62.25.21 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the arc

Re: Re: [gmx-users] problem with protein secondary structure analysis

Thanks to Justin for his prompt reply in .mdp file mentioned energy groups and tc-grps are protein and sol_cl . I am in doubt that first 250ps of md run it in npt condition later nvt till 7ns finally made into long .xtc file. I tried your suggested way in earlier post but I didnt get it. one

Re: [gmx-users] about how to set the environment variable

Hi beibei, When asking such questions, it is vital to provide information about your OS. Linux, Windows, Mac? Do you use (ba)sh, (t)csh or some other shell. Wouldn't hurt to understand a bit more about computers and terminology if your research depends on them. Linux: (ba)sh: export GMX_NO_SOLV_O

[gmx-users] about how to set the environment variable

Hi, all I read a message in the GROMACS mailing list, showing below: >Subject: RE: [gmx-users] cgnr >I have fixed the bug. >You can avoid the bug in the 3.3.1 release by setting the environment >variable: >GMX_NO_SOLV_OPT >Berk. which is from http://www.gromacs.org/pipermail/gmx-

Re: [gmx-users] tfe

shahrbanoo karbalaee wrote: Dear justin I trap in local minma.I dont know. I don't know either. Do you think there is some problem with your minimization? What happened when you minimized your structure? Now after edit topolgy file I get error again.not found C type.I make tfe.pdb and t

Re: [gmx-users] problem with protein secondary structure analysis

minnale wrote: Hi all, I intersted in analysing secondary structure of protein by using VMD and performed these steps. 1. First loaded min.gro file and corresponding min.xtc then all equalibration .xtc files till here MD movie has run fine. 2. I had long trajectory in a single file, so

[gmx-users] problem with protein secondary structure analysis

Hi all, I intersted in analysing secondary structure of protein by using VMD and performed these steps. 1. First loaded min.gro file and corresponding min.xtc then all equalibration .xtc files till here MD movie has run fine. 2. I had long trajectory in a single file, so cut it down in

[gmx-users] tfe

Dear justin I trap in local minma.I dont know. Now after edit topolgy file I get error again.not found C type.I make tfe.pdb and tfe.gro in prodrg and try it again editconf for change pdb to gro file. I saw source code toputil line 61.not found C type. best-- sh-karbalaee __

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Out of office AutoReply => August the 31th For urgent matters, please contact Colette Zeches: [EMAIL PROTECTED] +32(0)81-62.25.21 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the arc