----- Original Message ----- From: ms <deviceran...@gmail.com> Date: Wednesday, August 4, 2010 3:07 Subject: Re: [gmx-users] Required To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> On 03/08/10 17:32, Jafar Azamat wrote: > >When the program runs by > >"pdb2gmx" Option, the file X.top doesnot any information about force > >constant X.pdb file and I enter informations handling in this file. > > Your question does not make any sense, can you try to rephrase it? > > >In addition,How can I make in Gromacsa regular cluster > structure of a > >molecule ? > > > > > >Whether by > >g_cluster option? If this option could be to do this, > >please help me to make a cluster structure from a adamantine > molecule in a > >box > >in sizes: x=10, y=10, z=10 an put 125 number from adamantane > mulecule( in > >each > >direction 5 molecule means 5*5*5and > >distance every molecule of each other will be 1 nm) in this box. > > As far as I know, you can either try to use genbox with a > solvent different from water (i.e. your adamantane), or write a > script using editconf. You can find documentation online for both. genconf is a better match for what the OP is trying to do. Mark > g_cluster does a completely different thing (it clusters > together similar structures from a trajectory). > > cheers, > m. > -- > gmx-users mailing list gmx-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 post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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