Re: [gmx-users] simulation single molecule in water

2013-05-07 Thread Dr. Vitaly Chaban
cs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Souilem Safa > Sent: Tuesday, 7 May 2013 4:38 PM > To: Discussion list for GROMACS users > Subject: [gmx-users] simulation single molecule in water > > Dear gromacs users, > I'm simulating a single molecule in spc wa

RE: [gmx-users] simulation single molecule in water

2013-05-07 Thread Emanuel Birru
GROMACS users Subject: [gmx-users] simulation single molecule in water Dear gromacs users, I'm simulating a single molecule in spc water. I'm using a cubic water box which has 3.4 nm size. I got the toplogy of my molecule via PRODRG. After running minimization, NVT , NPT and MD for 10 ns ,

[gmx-users] simulation single molecule in water

2013-05-06 Thread Souilem Safa
Dear gromacs users, I'm simulating a single molecule in spc water. I'm using a cubic water box which has 3.4 nm size. I got the toplogy of my molecule via PRODRG. After running minimization, NVT , NPT and MD for 10 ns , I checked the density of water ,it was less than the real value (1000 kg m\S-3\