[gmx-users] Re: gmx-users Digest, Vol 54, Issue 83

The easiest is to use antechamber to generate your topology and then use the amb2gmx.pl (http://www.alchemistry.org/wiki/index.php/Image:Amb2gmx.gz) To convert your amber topology to gromacs. sevaas Message: 2 Date: Sat, 18 Oct 2008 00:23:07 -0200 From: Ragnarok sdf [EMAIL PROTECTED]

[gmx-users] Re: gmx-users Digest, Vol 51, Issue 21

In the [ defaults ] section change the combination rule. servaas Hi, Is there a possibility when constructing the own .itp file to point out Lennard-Jones (12, 6) parameters not in the form of C6 and C12 but as sigma and epsilon. Is there any key to switch this option? Thanks.

[gmx-users] Re: Dynamics : ONE dihedral angle time resolution

Or add option -all if you have several... servaas Message: 2 Date: Thu, 03 Jul 2008 10:36:56 +0200 From: Xavier Periole [EMAIL PROTECTED] Subject: Re: [gmx-users] Dynamics : ONE dihedral angle time resolution To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL

[gmx-users] pbc-replica exchange-trjconv

For a given temperature, I will make them continues again then before analysis. Thanks for the help! kind regards, servaas Hoi Servaas, Was that the trajectory for a given temperature, or for a given system? It should be for the latter, as otherwise, there will be weird shifts introduced.

[gmx-users] trjcat -demux

Dear gromacs users, I tried using trjcat like this: trjcat -f gromacs*.trr -demux replica_index.xvg (see below for replica_index.xvg and logfile) there are 20 trajectories containing each 2001 frames, with timestep of 0.5ps (I checked it with gmxcheck). The error: Reading frame 60

[gmx-users] Re: pbc-replica exchange-trjconv

the problem, this makes that there are jumps in the trajectory of course... kind regards, servaas servaas michielssens wrote: Dear gromacs users, I have a problem that is already discussed a lot on the mailing list, in a protein-ligand simulation the ligad jumps out of the box

[gmx-users] system contains proteins and DNAs with ffamber99

If you have amber, you can make your topology in amber and convert them to gromacs with the script on this website: http://chemistry.csulb.edu/ffamber/tools.html kind regards, servaas Dear all, Sometimes,the PDB file contains water molecules which only have the oxygen atom. Can

[gmx-users] pbc-replica exchange-trjconv

Dear gromacs users, I have a problem that is already discussed a lot on the mailing list, in a protein-ligand simulation the ligad jumps out of the box. The trajectory is generated by replica exchange simulation. So I used trjconv with the option cluster: trjconv -f fit.trr -o cluster.trr

[gmx-users] Re: Help needed on using general amber force field (GAFF)

. If you have such experience, please let me know. I do appreciate your kind help. best regards, Xiangyu On 3/14/08, servaas michielssens [EMAIL PROTECTED] wrote: I don't think you can generate your topology from the pdb file with gromacs in this case (with gaff). You can first make

[gmx-users] Re: Help needed on using general amber force field (GAFF) in Gromacs

I don't think you can generate your topology from the pdb file with gromacs in this case (with gaff). You can first make it in amber and than convert it to gromacs. On this website is the info you need, in the FAQs there is a link to dowload the script to do the job.

[gmx-users] gromacs versus amber boxsize

I ran the following command in gromacs: editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8 The equivalent command in amber: solvateoct p61_vac.pdb TIP3PBOX 8.0 As far as I understand this, both command created a box were the edges are 0.8 nm away from the solute. But the

[gmx-users] Re: parallel simulation crash on 6 processors

[EMAIL PROTECTED] Subject: Re: [gmx-users] parallel simulation crash on 6 processors To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed servaas michielssens wrote: I tried to run a gromacs

[gmx-users] parallel simulation crash on 6 processors

I tried to run a gromacs simulation (gromacs 3.3.1, MD, 18000 atoms) on 2 systems: Intel(R) Pentium(R) CPU 2.40GHz with 100Mbit network and AMD Opteron(tm) Processor 250 with 1Gbit network On both systems I had a crash when I tried to run with more then 5 processors. From 1-5 there was no

[gmx-users] Re: gmx-users Digest, Vol 43, Issue 81

Date: Wed, 21 Nov 2007 14:03:53 -0800 From: David Mobley [EMAIL PROTECTED] Subject: Re: [gmx-users] restart an amber run in gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Hi, servaas michielssens

[gmx-users] gromacs preformance versus amber

that amber could simulate 1.5ns/day and gromacs only 1ns/day. This was a surprise to me, I expected that gromacs would be faster. Could it be that using gromacs with the amberFF is not faster than just using amber? I am new to gromacs and perhaps I didn't compare them correct. kind regards, servaas

[gmx-users] restart amber run in gromacs

to run it after minimalization and this worked fine. So there seems to be a problem while converting the files, I am new to gromacs and I don't really have a clue how to find the cause of this problem, perhaps some of you also tried to continue a amber run in gromacs? kind regards, servaas

[gmx-users] restart an amber run in gromacs

to run it after minimalization and this worked fine. So there seems to be a problem while converting the files, I am new to gromacs and I don't really have a clue how to find the cause of this problem, perhaps some of you also tried to continue a amber run in gromacs? kind regards, servaas