[gmx-users] g_analyze

Hi users, I have got a data from g_mindist ie water and protein atom distance in each time frame. Now I have to find the auto correlation function using g_analyze but my output file from g_mindist has the time frame,water molecule number. How do I compute the ACF. In ACF data set the x axis is

[gmx-users] CfP: 2nd Workshop on Model-driven Approaches for Simulation Engineering (Mod4Sim), in Symposium on Theory of Modeling and Simulation, SCS Spring Sim 2012

CALL FOR PAPERS 2nd International Workshop on Model-driven Approaches for Simulation Engi

Re: [gmx-users] Error mesage

On 23/09/2011 11:18 PM, Tanos Franca wrote: Dear gmx users, Does someone know how to deal with the error mesage bellow ? With my best regards, Tanos C. C. Franca. Program mdrun, VERSION 4.5.4 Source code file: domdec_con.c, line: 693 Fatal error: DD cell 2 1 0 could only obtain 273 of the 275 a

[gmx-users] Error mesage

Dear gmx users, Does someone know how to deal with the error mesage bellow ? With my best regards, Tanos C. C. Franca. Program mdrun, VERSION 4.5.4 Source code file: domdec_con.c, line: 693 Fatal error: DD cell 2 1 0 could only obtain 273 of the 275 atoms that are connected via constraints from

Re: [gmx-users] problem in compiling GMX with MPI

thanks you,Mark the problem has been solved. I redefined the flag of openmpi, then gmx compliled successfully. -- Sincerely yours Dr Ji-Nan Niu School of Materials Science and Engineering. China University of Mining and Technology. Jiangsu Province, XuZhou 221116 P. R. China -- gmx-us

Re: [gmx-users] if PRODRG calculate incorrectly

On 23/09/2011 4:48 PM, ahmet y?ld?r?m wrote: Dear users, If I obtain/generate the topology file for a ligand using another program (except PRODRG); 1) How can I arrange .itp file? Because it seems very complicate. Yes, this is not an easy thing to do. Modelling an arbitrary organic compoun