[gmx-users] introducing ADP and ATP to Gromacs

dear users is there any way to introduce "ADP" and "ATP" to Gromacs? my protein holds these ligands. but they are not known to Gromacs. regards. Sajad -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.g

Re: [gmx-users] introducing ADP and ATP to Gromacs

On 4/25/2011 6:26 PM, Sajad Ahrari wrote: dear users is there any way to introduce "ADP" and "ATP" to Gromacs? my protein holds these ligands. but they are not known to Gromacs. Some of the GROMACS force fields have ATP. Otherwise, the advice here http://www.gromacs.org/Documentation/How-tos

Re: [gmx-users] dealing with ATP

dear Justin it seems that, ADP and ATP are not known to any of gromacs forcefields. but their topologies have been described in amber web site(as follows). should i be adding them to .tpr file of gromacs? if so, how can i access this file and is there any modification being needed in what amber

Re: [gmx-users] openmm 3.0, opencl support

Have you installed the CUDA Toolkit 4.0 ? I have never tried, just guessed. lina On Mon, Apr 25, 2011 at 9:17 AM, Claus Valka wrote: > Hello, > > I'm interested in knowing the level of development about gromacs supporting > the opencl framework language. > > I have read the manual about gromac

Re: [gmx-users] dealing with ATP

ATP is well 'known' and used, just put attention to it protionation state. Cheers, Itamar On 25/04/2011 8:05 PM, Sajad Ahrari wrote: dear Justin it seems that, ADP and ATP are not known to any of gromacs forcefields. but their topologies have been described in amber web site(as follows).

Re: [gmx-users] dealing with ATP

On 4/25/2011 8:05 PM, Sajad Ahrari wrote: dear Justin it seems that, ADP and ATP are not known to any of gromacs forcefields. but their topologies have been described in amber web site(as follows). should i be adding them to .tpr file of gromacs? if so, how can i access this file and is there

[gmx-users] trjcat eneconv time continuation

Hi, I am dealing with a special case of trajectory concatenation: I have several equilibration trajectories that their times are always restarted to 0, due employing different force constants for positional restraints, but using the output structure of the previous step as input anyway. Using trjc

[gmx-users] Re: error in g_x2top

Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. I am CC'ing this message there and ask that anything further be posted to the list. See below for comments. Zahra Kayani wrote: Dear, Dr.Lemkul command1:pdb2gmx -f shp2.pdb -o conf.gro it runs

Re: [gmx-users] trjcat eneconv time continuation

On 4/25/2011 8:42 PM, David Rodríguez wrote: Hi, I am dealing with a special case of trajectory concatenation: I have several equilibration trajectories that their times are always restarted to 0, due employing different force constants for positional restraints, but using the output structur

[gmx-users] tutorials of REMD

Dear GMX users, Are there some tutorials guiding how to do REMD simulations using gromacs? Thanks very much! All the best, qinghua -- 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

Re: [gmx-users] tutorials of REMD

fancy2012 wrote: Dear GMX users, Are there some tutorials guiding how to do REMD simulations using gromacs? Thanks very much! Google will tell you if there is any formal tutorial, otherwise a quick check of the Gromacs site turns up: http://www.gromacs.org/Documentation/How-tos/REMD -

Re: [gmx-users] trjcat eneconv time continuation

2011/4/25 Mark Abraham > On 4/25/2011 8:42 PM, David Rodríguez wrote: > >> Hi, >> >> I am dealing with a special case of trajectory concatenation: I have >> several equilibration trajectories that their times are always restarted to >> 0, due employing different force constants for positional res

Re: [gmx-users] openmm 3.0, opencl support

Hello, thank you for your prompt response. Unfortunately neither cuda toolkit 3.2 nor 4.0 was possible to be installed on my system. It required nvidia.co file. I think I just have to wait for an ati-opencl gromacs support. Regards, Nikos Von: lina An: Claus

Re: [gmx-users] trjcat eneconv time continuation

Hi David, You should have as many lines with a 'c' as you have trajectories. Cheers, Tsjerk On Apr 25, 2011 3:51 PM, "David Rodríguez" wrote: 2011/4/25 Mark Abraham > > On 4/25/2011 8:42 PM, David Rodríguez wrote: >>... Sorry that my query wasn't detailed enough. Trjcat yields a Fatal err

Re: [gmx-users] trjcat eneconv time continuation

2011/4/25 Tsjerk Wassenaar > Hi David, > > You should have as many lines with a 'c' as you have trajectories. > > Cheers, > > Tsjerk > Sure Tsjerk! Now options 2 and 3 (not 1) work, just that easy. Thank you so much. Best, David. > On Apr 25, 2011 3:51 PM, "David Rodríguez" > wrote: > > > > 2

Re: [gmx-users] trjcat eneconv time continuation

Hi David, Sorry for reading half... 'echo c c | trjcat ... ' should work. Cheers, Tsjerk On Apr 25, 2011 6:02 PM, "David Rodríguez" wrote: 2011/4/25 Tsjerk Wassenaar > > Hi David, > > You should have as many lines with ... Sure Tsjerk! Now options 2 and 3 (not 1) work, just that easy. Than

[gmx-users] Load imbalance vs accuracy

Hi Is load imbalance during mdrun only a performance issue or it affects accuracy of run as well? thanks sikandar -- 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/Sear

[gmx-users] Re: Potential energy methanol in a box

Thanks again for your response. I appreciate all your help. On Sat, Apr 23, 2011 at 6:11 PM, Fabian Casteblanco wrote: > Hello, > > I'm trying to fill a box with methanol using CHARMM FF Parameters.  I > also need to do this for ethanol and 1-propanol. > > For ethanol, each individual molecule h

Re: [gmx-users] Load imbalance vs accuracy

Hi, load imbalance is only a performance issue. Load balancing affects binary reproducibility (meaning the exact same value) but not accuracy (those it can differ but only within the same accuracy). Binary reproducibility should only be important for testing purposes, thus you should use load bal