[gmx-users] Pressure and box volume

Hello Justin! I was trying to getting down the pressure of my simulation from aprox 300 bar to 1 bar. I increased the box volume and now I have 27 bars but my density decrease dramatically from 970 to 320 kg/m3. I tried to add more water molecules to increase it again but then the pressure

Re: [gmx-users] Pressure in NPT simulation

Hello Justin, thanks for your help. The simulation has 250 steps (5000ps). Mishelle From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Sunday, March

Re: [gmx-users] Pressure in NPT simulation

On 3/19/17 3:17 PM, Mishelle Oña wrote: Hello, I have a question concerning pressure. I runned a NPT simulation with the following parameters: ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic tau_p= 1.01325 This is a rather

[gmx-users] Pressure in NPT simulation

Hello, I have a question concerning pressure. I runned a NPT simulation with the following parameters: ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic tau_p= 1.01325 compressibility = 4.5e-5 ref_p=

Re: [gmx-users] topology file construction

On 3/19/17 10:02 AM, abhisek Mondal wrote: Hi, I'm using following topology configuration for the above said heteroatom: 1OM 1 ANP O1G 1 -0.348 15.9994 2 P 1 ANP PG 10.971 30.9738 3OM 1 ANP O2G 1 -0.348

Re: [gmx-users] topology file construction

Hi, I'm using following topology configuration for the above said heteroatom: 1OM 1 ANP O1G 1 -0.348 15.9994 2 P 1 ANP PG 10.971 30.9738 3OM 1 ANP O2G 1 -0.348 15.9994 4OM 1 ANP O3G

[gmx-users] topology file construction

Hi, I'm trying to perform a protein-ligand MD run. But could not being able to construct a reliable topology file of the ligand. I've tried the PRODRG server but charges comes out so messed up. If I set uniform charges to same kind of atoms then also how can I validate if my ligand is