Re: [gmx-users] g_sas

On 2010-04-04 07.13, Chih-Ying Lin wrote: HI THe command => g_sas_mpi -f 6LYZ-MD566500.xtc -s 6LYZ-MD566500.tpr -o solvent-accessible-surface.xvg -oa atomic-sas.xvg -or residue-sas.xvg In the solvent-accessible-surface.xvg => @ s0 legend "Hydrophobic" @ s1 legend "Hydrophilic" @ s2 legend "To

[gmx-users] Re: configure error

Hello List, for the record, the issue could be fixed by regenerating the configure script with autoreconf version 2.13 (on a Debian (Squeeze) box). Thanks, Jerome BENOIT > Hello everyone, > > I tried to install gromacs on another cluster, after this, > > ./configure \ > --enable-shared

[gmx-users] gromacs, lam and condor

Hi, I tried to use 4 and 8 CPUs. There are about 6000 atoms in my system. The interconnect of our computer is the network with speed 1Gb but not optical fiber. I'm sorry for my poor English and I couldn't express well in my question. Everytime I submitted the parallel job, the nodes assigned

Re: [gmx-users] Potential Tables for user defined potentials

Hi all I have just been stuck on this very problem of user defined potentials. When I emailed this list I was asked if I could make notes on the solution as this is a problem that seems to come up a lot. Anyway, I will send the notes to you separately Sikandar and would ask if anyone knows where

Re: [gmx-users] Potential Tables for user defined potentials

Hi Gareth Thanks for the notes on user defined potentials in GROMACS. I will go through it and will send you the feedback after I get the simulation results. Thanks sikandar On Sun, Apr 4, 2010 at 11:27 AM, Gareth Tribello wrote: > Hi all > > I have just been stuck on this very problem of user

[gmx-users] DSSP=> how to edit .eps file

Hi With the following two commands, do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc secondary-structure.xvg xpm2ps -f secondary-structure.xpm -o secondary-structure.eps With GIMP, i can see the secondary structure plot. The legend indicates the color of different second str

Re: [gmx-users] DSSP=> how to edit .eps file

Chih-Ying Lin wrote: Hi With the following two commands, do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc secondary-structure.xvg xpm2ps -f secondary-structure.xpm -o secondary-structure.eps With GIMP, i can see the secondary structure plot. The legend indicates th

Re: [gmx-users] Potential Tables for user defined potentials

Gareth Tribello wrote: Hi all I have just been stuck on this very problem of user defined potentials. When I emailed this list I was asked if I could make notes on the solution as this is a problem that seems to come up a lot. Anyway, I will send the notes to you separately Sikandar and w

[gmx-users] g_sas

Hi g_sas computes hydrophobic, hydrophilic and total solvent accessible surface area. I chose => protein for calculation group => protein for output group what does it define "hydrophobic solvent accessible surface area"? => does that, the surface area, enclose the hydrophobic atoms/

[gmx-users] g_sas

Hi >From David, "If you select a group consisting of a single residue in a protein the SAS will be computed as if the rest of the protein is not there. Very useful when you want to compute protein-protein interface areas." => therefore, if i select a group consisting of a single residue, which is

[gmx-users] DSSP=> how to edit .eps file

HI How to pass an .m2p file to xpm2ps to change the dimensions of the plot, data point size, etc. ??? Thank you Lin Chih-Ying Lin wrote: > > Hi > With the following two commands, > > do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc secondary-structure.xvg > > xpm2ps -f sec

Re: [gmx-users] DSSP=> how to edit .eps file

Chih-Ying Lin wrote: HI How to pass an .m2p file to xpm2ps to change the dimensions of the plot, data point size, etc. ??? Use the -di flag of xpm2ps. http://manual.gromacs.org/current/online/m2p.html -Justin Thank you Lin Chih-Ying Lin wrote: Hi With the following two commands,

Re: [gmx-users] gromacs, lam and condor

Hi Hsin-Lin, As Mark answered already yesterday: 1) 1Gb Ethernet is not fast enough for more than 2 or maximum 4 CPUs. (and if each process of mdrun has to wait ~90% of the time to get data from the others, then you result in just 10% load, right? ) 2) telling from the line: >> > /stathome/jiangs