[gmx-users] Re: Extending water in negative Z direction

Hi ALL, Thanks for the reply. I think what I mean will be more clear by just having a look at the structure (attached). I have tried by increasing the Z value, as suggested by David, but that only extends the water on one side of the bilayer only and not on the other side (which I need).

Re: [gmx-users] Re: Extending water in negative Z direction

Anirban Ghosh wrote: Hi ALL, Thanks for the reply. I think what I mean will be more clear by just having a look at the structure (attached). I have tried by increasing the Z value, as suggested by David, but that only extends the water on one side of the bilayer only and not on the other

Re: [gmx-users] Re: Extending water in negative Z direction

Anirban, Please, many of us have years of experience with MD and this type of systems. If you had considered that, rather than assuming that we still don't understand what you mean, you would have been on the right track to fix an apparent caveat in your knowledge regarding MD simulations, and

Re: [gmx-users] diffusion coefficient with g_msd

On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote: Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate the diffusion coefficient of the molecules inside the membrane, and therefore I looked at

Re: [gmx-users] Scaled 1-5 interactions

On Fri, Jun 05, 2009 at 10:31:22AM +1000, Mark Abraham wrote: Setting the number of exclusions for a moleculetype to 4, in a forcefield with generate_pairs = yes and fudgeLJ = 0.5 will probably see pdb2gmx get everything except the 1-5 interactions right. Then you post-process the .top from

Re: [gmx-users] g_hbond error

Justin A. Lemkul skrev: krishnakumar wrote: Hi, Has any one encountered this error while using g_hbond? * Select a group: 12 Selected 12: 'SOL' Select a group: 12 Selected 12: 'SOL' Calculating hydrogen bonds in SOL (20949

SV: [gmx-users] diffusion coefficient with g_msd

Dear XAvier, Thank you very much for your answer. I have posted my .mdp file in the bottom of the email - as I haven't specified comm_mode or nstcomm, the default values should be used - this is also confirmed in the .log file: nstcomm = 1 comm_mode= Linear

[gmx-users] conversion to tip5p

Hi, all Using gromacs 3.3 I try to work with tip5 water, but I fail to convert water molecules of gro-file to tip5 kind. Conversion to tip4p from spc is easy with pdb2gmx pdb2gmx -f my_spc.gro -water tip4p -o my_tip4.gro -p my_tip4.top , but when I apply similar command for tip5p, the output

Re: SV: [gmx-users] diffusion coefficient with g_msd

Sarah Witzke wrote: Dear XAvier, Thank you very much for your answer. I have posted my .mdp file in the bottom of the email - as I haven't specified comm_mode or nstcomm, the default values should be used - this is also confirmed in the .log file: nstcomm = 1

Re: [gmx-users] conversion to tip5p

2009/6/5 Dmitri Dubov ddu...@ngs.ru Hi, all Using gromacs 3.3 I try to work with tip5 water, but I fail to convert water molecules of gro-file to tip5 kind. Conversion to tip4p from spc is easy with pdb2gmx pdb2gmx -f my_spc.gro -water tip4p -o my_tip4.gro -p my_tip4.top Does it really

Re: [gmx-users] conversion to tip5p

Dmitri Dubov wrote: Hi, all Using gromacs 3.3 I try to work with tip5 water, but I fail to convert water molecules of gro-file to tip5 kind. Conversion to tip4p from spc is easy with pdb2gmx pdb2gmx -f my_spc.gro -water tip4p -o my_tip4.gro -p my_tip4.top , but when I apply similar

[gmx-users] Pressure and NVT Simulations

Hi, I am trying to equilibrate a box of SPC/E water using NVT simulations. After 2 ns of equilibration my pressure is still 0 bars. Is it an expected behavior for NVT simulations or the pressure should converge to the thermodynamic equilibration value corresponding to T and density after a finite

Re: [gmx-users] Pressure and NVT Simulations

On Fri, 2009-06-05 at 23:28 +0530, Manik Mayur wrote: Hi, I am trying to equilibrate a box of SPC/E water using NVT simulations. After 2 ns of equilibration my pressure is still 0 bars. Is it an expected behavior for NVT simulations or the pressure should converge to the thermodynamic

Re: [gmx-users] Pressure and NVT Simulations

On Fri, Jun 5, 2009 at 11:58 PM, Jussi Lehtola jussi.leht...@helsinki.fiwrote: On Fri, 2009-06-05 at 23:28 +0530, Manik Mayur wrote: Hi, I am trying to equilibrate a box of SPC/E water using NVT simulations. After 2 ns of equilibration my pressure is still 0 bars. Is it an expected

Re: [gmx-users] Pressure and NVT Simulations

On Sat, 2009-06-06 at 00:30 +0530, Manik Mayur wrote: On Fri, Jun 5, 2009 at 11:58 PM, Jussi Lehtola jussi.leht...@helsinki.fi wrote: Generally speaking, if your density is too small, the system wants to increase it and thus you have negative pressure. If it is too

Re: [gmx-users] Scaled 1-5 interactions

* Mark Abraham mark.abra...@anu.edu.au [2009-06-05 10:31:22 +1000]: Borys Szefczyk wrote: Dear GROMACS Users, I would like to use the OPLS force field, but with additional scaling factor for the Coulomb 1-5 interactions for certain atoms. More precisely, I want to use the standard 0.5 scaling

SV: SV: [gmx-users] diffusion coefficient with g_msd

Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole Sendt: fr 05-06-2009 13:32 Til: Discussion list for GROMACS users Emne: Re: SV: [gmx-users] diffusion coefficient with g_msd Sarah Witzke wrote: Dear XAvier, Thank you very much for your answer. I have posted my .mdp file in

Re: SV: SV: [gmx-users] diffusion coefficient with g_msd

Sarah Witzke wrote: Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole Sendt: fr 05-06-2009 13:32 Til: Discussion list for GROMACS users Emne: Re: SV: [gmx-users] diffusion coefficient with g_msd Sarah Witzke wrote: Dear XAvier, Thank you very much for your answer. I have