[gmx-users] itp files in membrane simulation

Dear all, I want to use lipid.itp dmpc.itp for a bilayer simulation, and I have gathered this information so far that one has to manually modify these itp files in order to use the latest force fields, ie, G43a2 etc. Does this include lipid.itp file too which involves various lipid-GROMOS

[gmx-users] membrane set up!!!

The below-mentioned lines (from forum) do not work for me!! I am dealing with DMPC instead of POPC and I hope that is not making any difference!! kindly help, Priyanka S. Hu Ugur, actually you don't have to care to run the lipid pdb by Tieleman through pdb2gmx at all - just copy the respective

[gmx-users] problem still lies regarding dssp

Dear All, I do not know whether I am interrupting you again and again by asking the same question, but I am helpless , I can not detect my fault, When I run the program DSSP it works fine, but while executing do_dssp or my_dssp (as suggested by Yang) the program seems to be

RE: [gmx-users] problem still lies regarding dssp

Hi Sangeeta, Let me ask you few questions in order to solve the problem. Are you sure your do_dssp prog were running or it was hanged? To make sure please try using verbose output using -v option. Is your computer shared among too many people? What is the file permission status of dssp? To

[gmx-users] loss of information trr xtc

hi guys. can anyone tell me if there is a loss of information when i convert a trr file into a less-storage-consuming xtc file ? can i reconevrt the xtc file into trr again and then have no loss of information ? thanks for a very short answer Greetings Joern

Re: [gmx-users] problem still lies regarding dssp

sangeeta kundu wrote: Dear All, I do not know whether I am interrupting you again and again by asking the same question, but I am helpless , I can not detect my fault, When I run the program DSSP it works fine, but while executing do_dssp or my_dssp (as suggested by Yang) the

[gmx-users] Pressure coupling question

Hello, I am simulating a lipid bilayer system, and am having some trouble understanding the pressure output. When I run a simulation, even when I do not add any perturbations or fix any atoms, the pressure oscillations are quite large. The temperature coupling seems fine. After about 1ps,

Re: [gmx-users] Pressure coupling question

toma0052 wrote: Hello, I am simulating a lipid bilayer system, and am having some trouble understanding the pressure output. When I run a simulation, even when I do not add any perturbations or fix any atoms, the pressure oscillations are quite large. The temperature coupling seems fine.

[gmx-users] gromacs-3.3 build on linux. make fails

Hello, I'm new to this list and hope I can get some help. I'm seeking help with installing double precision gromacs-3.3 on Centos-4 linux. I'm using Lam-7.1.2 built with gcc4. I built fftw with this configure string which succeeded: ./configure --prefix=/usr/local/fftw301-double

[gmx-users] Urey bradley term in the sum of energies

Hello everybody, I've got an awful doubt on how the Urey-Bradley (UB) term is taken into account in the potential energy. When an angle has got regular and UB parameters, how this will appear in the .edr file? The angle energy will only appear in the UB term only or it will be splitted between

Re: [gmx-users] Urey bradley term in the sum of energies

Nicolas SAPAY wrote: Hello everybody, I've got an awful doubt on how the Urey-Bradley (UB) term is taken into account in the potential energy. When an angle has got regular and UB parameters, how this will appear in the .edr file? If you have a force field with both angle function 1 and angle

Re: [gmx-users] gromacs-3.3 build on linux. make fails

susan james wrote: Hello, I'm new to this list and hope I can get some help. Thanks for the good help request - lots of pertinent information can only improve your chances of getting help! the gromacs make fails. the complete log is too large to send. and, more precisely, here's where

Re: [gmx-users] gromacs-3.3 build on linux. make fails

susan james wrote: Hello, I'm new to this list and hope I can get some help. I'm seeking help with installing double precision gromacs-3.3 on Centos-4 linux. I'm using Lam-7.1.2 built with gcc4. I built fftw with this configure string which succeeded: ./configure

Re: [gmx-users] gromacs-3.3 build on linux. make fails

here's a bit more(below) of the make build that failed. I've captured the last lines. I think it may indeed have something to do with gcc4. mpicc is in the path. I'm wondering if I should set this variable: CC=gcc4 instead of CC=mpicc any ideas on this?

Re: [gmx-users] gromacs-3.3 build on linux. make fails

susan james wrote: here's a bit more(below) of the make build that failed. I've captured the last lines. I think it may indeed have something to do with gcc4. mpicc is in the path. I'm wondering if I should set this variable: CC=gcc4 instead of CC=mpicc any ideas on this? you do want to