[gmx-users] PRODRG -cgnr

Dear gromacs users I wan to use PRODRG server to do md simulation of my system (drug-protein complex). I know charge and cgnr parameters obtained from PRODRG (for ligand molecule) are not accurate. I know there are 2 ways to solve this problem: 1) If there are special functional groups in my

Re: [gmx-users] PRODRG -cgnr

On 7/27/14, 11:49 AM, Atila Petrosian wrote: Dear gromacs users I wan to use PRODRG server to do md simulation of my system (drug-protein complex). I know charge and cgnr parameters obtained from PRODRG (for ligand molecule) are not accurate. I know there are 2 ways to solve this problem:

[gmx-users] How do I get to know the meaning of the first column in log file?

For example, in the following form, what does Wait + Comm. F mean? Is there a webpage that explains the forms in log file? R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Th. Count Wall t (s) G-Cycles %

Re: [gmx-users] How do I get to know the meaning of the first column in log file?

On Jul 28, 2014 4:53 AM, Theodore Si sjyz...@gmail.com wrote: For example, in the following form, what does Wait + Comm. F mean? Is there a webpage that explains the forms in log file? Unfortunately not (yet), but they correspond in a more-or-less clear way to the segments in manual figure

Re: [gmx-users] How do I get to know the meaning of the first column in log file?

Thanks a lot! But I am still confused about other things. For instance, what do count, wall t(s) G-Cycles mean? It seems that the last column is the percentage of G-Cycles. I really hope there is a place where I can find all relative information of the log file. 于 2014/7/28 11:12, Mark

[gmx-users] Some columns in log file.

Hi all, In the log file, what do count, wall t(s) G-Cycles mean? It seems that the last column is the percentage of G-Cycles. I really hope there is a place where I can find all relative information of the log file. Thanks in advance. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] lipid restrain

hello every one i got the solution it s not for -nt its for X we have to use core of workstation and in my system it is 4 so command is mdrun -nt 4 -deffnm npt and its working On Sat, Jul 26, 2014 at 12:41 PM, RINU KHATTRI nickname.mi...@gmail.com wrote: hello everyone its working simply

Re: [gmx-users] Error in system_inflate.gro coordinates does not match

hello everyone i used editconf editconf -f protein.gro -o protein_newbox.gro -box (membrane box vectors) -center *x y z* but in z axis i have been increased box size 10. (previously it is 6.23910 6.17970 6.91950