Re: [gmx-users] Thought you'd find this interesting

Hi, I doubt that a technical mailing list is the right place to advertise charity stuff. Especially if that means subscribing the mailing list to a newsletter. I try to keep up reading this mailing list, scanning for topics of interest to me, which becomes increasingly more difficult if I

Re: [gmx-users] Thought you'd find this interesting

Dear all gmxuser, I am extremely sorry for the post shared in the gmxuser mailing list. This was done by mistake. Please ignore the previous mail. I strongly apologize for the mail and the inconvenience caused. Anil On 24 June 2013 12:50, Oliver Schillinger o.rus...@fz-juelich.de wrote: Hi,

[gmx-users] TPI Results differ in v4.5.7 and v4.6.1

Hi GMX Users, We are computing the chemical potential of different gas molecules in a polymer melt with the tpi integrator. The computations are done for CO2 and CH4. The previous computations were done with v4.5.5 or 4.5.7 and gave equal results. I recently switched to gromacs version 4.6.1,

[gmx-users] problem with charmm2gromacs-pvm.py

Hello: I am trying to use charmm2gromacs-pvm.py to generate cgenff with comman: python charmm2gromacs-pvm.py toppar/par_all36_cgenff.prm toppar/top_all36_cgenff.rtf but it always failed with messages: Creating cgenff-2b7.ff files... Traceback (most recent call last): File

Re: [gmx-users] TPI Results differ in v4.5.7 and v4.6.1

Niels, This is very interesting. At our group, a colleague of mine and I have also identified differences in the TPI integrator between 4.0.X and 4.5.X, but we still haven't had the time to report it properly, since we are using a slightly modified version of the TPI algorithm. Instinctively, we

[gmx-users] radial distribution function gAB (r, theta)

Gromacs manual explains radial distribution function gAB (r, theta) but g_rdf donot have options to directly do this. Can anyone elaborate this. -- Best regards Neshatul Haque PhD, Dpt of Biotechnology university of hyderabad -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] TPI Results differ in v4.5.7 and v4.6.1

Hi João, Indeed your instinct seems to be good! When switching the Coulomb-Type to Cut-Off, there doesn't seem to be a difference between 4.6 and 4.5. Apparently its an issue with the PME sum. We will investigate further. Am 24.06.2013 um 14:42 schrieb João M. Damas jmda...@itqb.unl.pt:

Re: [gmx-users] Gromacs GPU system question

I strongly suggest that you consider the single-chip GTX cards instead of a dual-chip one; from the point of view of price/performance you'll probably get the most from a 680 or 780. You could ask why, so here are the reasons: - The current parallelization scheme requires domain-decomposition to

Re: [gmx-users] Gromacs GPU system question

On Sat, Jun 22, 2013 at 5:55 PM, Mirco Wahab mirco.wa...@chemie.tu-freiberg.de wrote: On 22.06.2013 17:31, Mare Libero wrote: I am assembling a GPU workstation to run MD simulations, and I was wondering if anyone has any recommendation regarding the GPU/CPU combination. From what I can see,

[gmx-users] Re: gmx-users Digest, Vol 110, Issue 114

I am using Red Hat Enterprise Linux 5.5 Raji On 6/20/13 5:16 PM, gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit

Re: [gmx-users] radial distribution function gAB (r, theta)

On 6/24/13 9:05 AM, neshat haq wrote: Gromacs manual explains radial distribution function gAB (r, theta) but g_rdf donot have options to directly do this. Can anyone elaborate this. That section probably refers to a feature that was intended to be included but was never developed. Such

Re: [gmx-users] Error while using genion

Please do not reply to the entire digest. It gets hopelessly confusing. On 6/24/13 10:51 AM, Raji Viswanathan wrote: I am using Red Hat Enterprise Linux 5.5 Raji Something about your shell environment is probably hosed. Do other commands that prompt for interactive input work, or just

[gmx-users] Re: Error while using genion

Yes, that command works and the entry 13 is recognized as 'SOL' -- View this message in context: http://gromacs.5086.x6.nabble.com/Re-gmx-users-Digest-Vol-110-Issue-114-tp5009358p5009361.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list

Re: [gmx-users] Re: Error while using genion

On 6/24/13 11:36 AM, raji_yu wrote: Yes, that command works and the entry 13 is recognized as 'SOL' OK, then you need to figure out why your shell doesn't understand the difference between an input stream and a command, otherwise you have to do all your selections via echo, which can be

Re: [gmx-users] TPI Results differ in v4.5.7 and v4.6.1

If you have a solid example that reproduced the problem, feel free to file an issue on redmine.gromacs.org ASAP. Briefly documenting your experiments and verification process on the issue report page can help help developers in giving you faster feedback as well as with accepting the report as a

[gmx-users] 1-4 interactions free energy calculations

Hi all! I have been running a series of simulations for coupling a molecule (free energy calculations). All my settings and parameters in the mdp file worked great for one system, but then I change the molecule to a bigger one and I started to have warnings about 1-4 interactions: Warning: 1-4

Re: [gmx-users] 1-4 interactions free energy calculations

On 6/24/13 1:07 PM, Sonia Aguilera wrote: Hi all! I have been running a series of simulations for coupling a molecule (free energy calculations). All my settings and parameters in the mdp file worked great for one system, but then I change the molecule to a bigger one and I started to have

[gmx-users] Settles vs. 3 normal constraints (energy conservation problem)

Dear All, I have a box of 3073 tip4p water molecules. I do a 250ps nvt, then 250 ps npt and finally a 1 ns nve (production run). I used the opls forcefield and I copied the tip4p.itp to my working directory (in order to be able to make changes). In one case I used the [ settles ] directive to