[gmx-users] genion problem with divalent ions

Hi, I just encountered (another) strange thing with genion. I wanted to neutralized a system by adding Mg-Ions (charge in ions.itp: 2, forcefield amber99sb), so I expected half of the system charge (-52) to be added as ions. BUT it added the same amount, i.e. 52 Mg ions instead of 26 which

Re: [gmx-users] Effect of refcoord_scaling

. Could you provide your mdp-file for us to look at? Best, Erik 6 sep 2012 kl. 00.31 skrev Matthias Ernst: Hi Chris, thank you for your answer. Let me comment on some of your hints. refcoord_scaling is only required when you are also using positions restraints. Therefore we need to know what

Re: [gmx-users] Effect of refcoord_scaling

The problem could be gen_vel=no if you are not loading velocities that are consistent with your production temperature of 200 K. If, for example, you do not load any velocities at all, then the initial forces will quickly be scaled up to reach 200 K and this can cause large scale

Re: [gmx-users] Effect of refcoord_scaling

of refcoord_scaling and can they be seen or detected easily? Thank you very much for your help, Matthias Ernst -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting

[gmx-users] Effect of refcoord_scaling

and can they be seen or detected easily? Thank you very much for your help, Matthias Ernst -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting

Re: [gmx-users] checkpoint file

Long story short: backup everything (since it's a backup, and hopefully you won't need it), then use the [whatever].cpt file. You don't want to do work twice, do you? If you use the [whatever]_prev.cpi file, you will calculate some frames *again* that are already there. If you use an up-to-date

Re: [gmx-users] checkpoint file

output and the issued command terminates in the terminal. Do I have to remove the -o -c -g -e -x flags from the command line? Appreciate your help, On 13 August 2012 15:28, Matthias Ernst matthias.ern...@student.kit.edu wrote: Long story short: backup everything (since it's a backup

Re: [gmx-users] pdb to xyz file format

Why do you want to use Gromacs? I would suggest to use openBabel, which can convert a whole bunch of file formats... Regards, Matthias Am 10.06.2012 16:55, schrieb Lara Bunte: Hi Is it possible to convert a .pdb file to a .xyz file with GROMACS? At this point there shouldn't be a force

[gmx-users] Question regarding genion

system (with -c 0.001, it will add 53 NA and 1 CL ions, meaning resulting salt concentration is 0). I use the amber99sb forcefield. Is this behaviour desired and do I miss the point of the -neutral option not working without specifying a concentration? Thanks for your help, Matthias Ernst

[gmx-users] Simulation protocol for Protein-DNA-complex

Hi, I have a question regarding simulation of a protein-DNA-complex where the protein encloses the DNA double helix. I did not find a tutorial for a system of three rather big molecules like these, that's why I ask. If there is such, I would appreciate a hint. I want to start with a crystal

Re: [gmx-users] Amber99bsc0

It is possible but not yet included in Gromacs. As far as I know, there are several people working on porting this forcefield to Gromacs (I have been searching for this myself last year). Check the archives for parmbsc0 and Gromacs and search for papers that include these terms. then you will

[gmx-users] Forcefield question

Hi, I am currently working with the AMBER forcefields provided by GROMACS. I noticed there are atoms in the forcefields (e.g. amber99 or amber03) with LJ parameters of 0.0 for sigma and epsilon. For example, the HO atom type is sometimes used (e.g. in SER or in the terminal Hs of DNA

[gmx-users] No automatic terminus detection

Hi, I try to simulate DNA or better parts of a long DNA double-helix. Therefore, the system I use is not correctly terminated at the ends from chemical point of view with OH-groups but rather cut out the longer helix. Nevertheless, all residues are named correctly, all atoms needed in the

Re: [gmx-users] No automatic terminus detection

tells me that this is impossible, so I have to change my system. That's not really what I expected (in fact, from a programmer's view, I think it should be no problem to leave out terminus search) but thanks for your help. Matthias Ernst -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Nucleic Acid in vacuo

in Gromacs? Thanks and best regards, Matthias Am Montag, den 12.09.2011, 14:37 +0200 schrieb Justin A. Lemkul: Matthias Ernst wrote: Dear Gromacs users, I am currently working on porting forcefields from Gromacs to another program with the aim of simulating DNA. Therefore, I wrote

[gmx-users] Nucleic Acid in vacuo

and the order of magnitude of the Coulomb term. Why is that? What does the SR in LJ and Coulomb in the Gromacs output mean? Any help would be thankfully apreciated. Best regards, Matthias Ernst -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please