[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 (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/Support/Mailing_Lists
[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 temperature and pressure? Thank you in advance, Turgay -- 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 (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/Support/Mailing_Lists
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 equilibration runs to arrive correct temperature and pressure? Equilibration is always advisable, though for a system of water you don't do any sort of position-restrained steps as you would if there were a solute. In any case, if you do not run explicit NVT and/or NPT phases, you'll have to throw out some of the beginning of the production trajectory anyway, since generation of velocities does not guarantee that you maintain any sort of equilibrated state, so the beginning of the run is equilibration. For stability reasons, NVT and NPT are advisable. Water is pretty robust, but why take a chance when equilibration steps are fast to do? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 (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/Support/Mailing_Lists
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 did geometry optimization for nsteps= 5. Now, can I continue with production run or do I need to do equilibration runs to arrive correct temperature and pressure? Equilibration is always advisable, though for a system of water you don't do any sort of position-restrained steps as you would if there were a solute. In any case, if you do not run explicit NVT and/or NPT phases, you'll have to throw out some of the beginning of the production trajectory anyway, since generation of velocities does not guarantee that you maintain any sort of equilibrated state, so the beginning of the run is equilibration. For stability reasons, NVT and NPT are advisable. Water is pretty robust, but why take a chance when equilibration steps are fast to do? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 (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/Support/Mailing_Lists -- 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 (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/Support/Mailing_Lists
[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 would like to automate this process so having a look at the description of the format would be a great help. Thank you. -- 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 (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/Support/Mailing_Lists
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 creating the .gro files by trial and error. I would like to automate this process so having a look at the description of the format would be a great help. The online manual describes all file formats (http://manual.gromacs.org) but unfortunately all Gromacs sites appear to be down at the moment. In any case, you can access the same information from the HTML files in your Gromacs installation, in the share/gromacs/html/online subdirectory. Open up gro.html in a web browser. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 (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/Support/Mailing_Lists
[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 Gromacs to psf files or anything and run under ACEMD? Thank you, Steven -- 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 (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/Support/Mailing_Lists
[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 OPLS-AA force field with fourierspacing = 0.10. and the md-vv integrator. I am running gromacs 4.5.5 compiled from the tarball on gromacs.org To try and track it down I ran a 100ps NVE simulation outputting coordinates and velocities every 1ps. I then used the trr trajectory file and ran: $ mdrun_d -s nve_short.tpr -rerun reference.trr -deffnm 8_cores -reprod -nt 8 $ mdrun_d -s nve_short.tpr -rerun reference.trr -deffnm 4_cores -reprod -nt 4 $ mdrun_d -s nve_short.tpr -rerun reference.trr -deffnm 1_cores -reprod -nt 1 then: $ g_energy_d -f 8_cores.edr -o 8_cores.xvg EOF 10 11 12 13 14 15 EOF etc. Where nve_short.tpr is the input file used for the original simulation and reference.trr is the trajectory it produced (I did not output forces into this which was an oversight). These were run on my machine a quad core hyper-threaded intel xeon. I also used performed the rerun on our local cluster on 12, 24, and 36 cores (dual 6 core intel xeon nodes with infiniband interconnects) The resulting energy files are significantly different energies for these snapshots summarised in this table: number of cores, Potential Energy,Standard Deviation reference 7912.74479607 180.525445863 1_cores9635.92644669 180.525445891 4_cores1061.8467459 244.14154375 8_cores 776.470114871 208.368028756 12_cores374.243502525 204.012539953 24_cores667.44876102 502.041766722 36_cores616.93105205 476.190500738 (reference is the energy extracted from the original simulation run on a 12 core node) The large variation in standard deviation means that these energies are not simply shifted but behaving differently which is apparent from a plot of the potential energies. has anyone else noticed any sort of inconsistency? Does anyone have any advice about what might cause this? Am I doing anything stupid? Thanks, Richard -- 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 (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/Support/Mailing_Lists
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 statement in the manual, but no further explanation. Anyone cares to expand on it ? For testing, I've recently performed a run with compressibility=0 for z and non-zero for x/y (so, exactly opposite to what the manual suggests :)). The box deformed as expected in x/y and the pressure seemed to be maintained correctly. Is there some reason for which this would be a random (i.e. not easily reproducible) result ? Or are there some less obvious problems with it ? I am trying to use walls with lipid bilayers. I once also applied a non-zero compressibility to x/y , and my bilayer physically collapsed in less than 1ns, although the simulation appeared to be otherwise nominal. Another thing I noticed was that the value of wall_density is important, since a small leakage past the wall may not be noticeable until you exceed 1-10ns and that will quickly drop volume to 0 and make it look like x/y has collapsed (and cause a system crash due to exceeding pme/dd tolerances). -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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 (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/Support/Mailing_Lists
[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! * 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/Support/Mailing_Lists
