[gmx-users] Re: gmx-users Digest, Vol 101, Issue 17

Dears Justin and Christopher Thanks a lot, I'll do the same. Sincerely -- 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! * Please don't post

[gmx-users] a box of water

Hi all, I want to do Molecular dynamics simulation of a box of water (SPC type). I get the spc216.pdb file from the gromacs/share/tutor. Firstly, I did geometry optimization for nsteps= 5. Now, can I continue with production run or do I need to do equilibration runs to arrive correct

Re: [gmx-users] a box of water

On 9/7/12 7:34 AM, Turgay Cakmak wrote: Hi all, I want to do Molecular dynamics simulation of a box of water (SPC type). I get the spc216.pdb file from the gromacs/share/tutor. Firstly, I did geometry optimization for nsteps= 5. Now, can I continue with production run or do I need to do

Re: [gmx-users] a box of water

Thanks a lot for your quick reply Justin. I got it. Turgay 2012/9/7 Justin Lemkul jalem...@vt.edu: On 9/7/12 7:34 AM, Turgay Cakmak wrote: Hi all, I want to do Molecular dynamics simulation of a box of water (SPC type). I get the spc216.pdb file from the gromacs/share/tutor. Firstly, I

[gmx-users] .gro file format details

Good day, I was looking for the documentation for the .gro format but I couldn't find it on the site or manual. I am missing something?I am trying to parametrize some lipid ligands using ATB (http://compbio.biosci.uq.edu.au/atb) and I have been creating the .gro files by trial and error. I

Re: [gmx-users] .gro file format details

On 9/7/12 11:42 AM, Julio Dominguez wrote: Good day, I was looking for the documentation for the .gro format but I couldn't find it on the site or manual. I am missing something?I am trying to parametrize some lipid ligands using ATB (http://compbio.biosci.uq.edu.au/atb) and I have been

[gmx-users] from GMX to NAMD/Amber

Dear All, I want to use ACEMD software on GPUs which I have an access to. It could take while before I would prepare system of interest in NAMD or Amber Tool as I always used Gromacs. Do you know whether there is an easy way to translate gro/pdb files (equilibrated) and topology prepared in

[gmx-users] Energies in simulation and rerun using different core counts

Dear All, I've been having some issues with energies with gromacs running on various core counts for a 7469 polymer in solvent system, constraining all bonds and running with a 2fs time step. I used PME-shift (1.05nm, 1.10nm), and a shift with the same parameters for the VdW, I am using the

Re: [gmx-users] MD problem with nwall=2

On 2012-09-06 02:46:21PM +0200, Bogdan Costescu wrote: On Wed, Sep 5, 2012 at 8:37 PM, Peter C. Lai p...@uab.edu wrote: Could be a result of not setting x/y compressibility = 0 as the manual suggests you should do... As one who has also tried to use walls recently, I've also found this

[gmx-users] Re: .gro file format details

Thank you, Justin. I haven´t thought of that. Best regards. -- 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!