Re: [gmx-users] uneven distribution of water across the bilayer

Alok wrote: Dear All, I am trying to simulate lipid-water system (340 POPE lipids & 6120 TIP4P Waters), during the solvation by genbox, It also add the the water at the interior of the bilayer. I removed those water molecules by my perl script. But after removing these water molecules I have

[gmx-users] uneven distribution of water across the bilayer

Dear All, I am trying to simulate lipid-water system (340 POPE lipids & 6120 TIP4P Waters), during the solvation by genbox, It also add the the water at the interior of the bilayer. I removed those water molecules by my perl script. But after removing these water molecules I have observed a zon

Re: [gmx-users] install problem on IBM powerpc AIX 5.3

Mark Abraham wrote: liu xin wrote: Hi Mark After some search on the web, I found that in AIX OS mpcc is the MPI c compiler, while mpCC is the MPI C++ compiler and mpxlf is the MPI fortran compiler. but when I tried to configure it like: " configure --enable-mpi MPICC=/usr/bin/mpcc", I still g

Re: [gmx-users] install problem on IBM powerpc AIX 5.3

liu xin wrote: Hi Mark After some search on the web, I found that in AIX OS mpcc is the MPI c compiler, while mpCC is the MPI C++ compiler and mpxlf is the MPI fortran compiler. but when I tried to configure it like: " configure --enable-mpi MPICC=/usr/bin/mpcc", I still got error complaining

Re: [gmx-users] install problem on IBM powerpc AIX 5.3

Hi Mark After some search on the web, I found that in AIX OS mpcc is the MPI c compiler, while mpCC is the MPI C++ compiler and mpxlf is the MPI fortran compiler. but when I tried to configure it like: " configure --enable-mpi MPICC=/usr/bin/mpcc", I still got error complaining "Cannot compile and

Re: [gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel

himanshu khandelia wrote: Check out http://wiki.gromacs.org/index.php/Doing_Restarts Thanks very much. I do understand the general restarting mechanism. It is only the first restart that was a little bit confusing > > I j

Re: [gmx-users] qasi-harmonic entropy calculation

Maybe there has been some mistake during your calculations? No, g_covar gives the average covariance matrix. You can check this matrix with the command -ascii. If you have used your own program to calculate entropy double check units conversion stuff. Regards. Pedro. 2007/10/18, Naser, Md Abu <[

RE: [gmx-users] qasi-harmonic entropy calculation

Hi David, Thanks for your information and I will have a look CVS head version. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAI

RE: [gmx-users] qasi-harmonic entropy calculation

Hi Pedro, Thank you for your attention to my email. Yes, I am using Schlitter equation and the rusult is cumulative. The entropy is meant to be decreased as the protein is stick on to a surface. I have used the entire protein as a subset. Is the programme takes the final structure for calcu

Re: [gmx-users] qasi-harmonic entropy calculation

Pedro Alexandre de Araújo Gomes Lapido Loureiro wrote: Hi, I understand you are using the Schlitter equation, is that so? Could you give more details? Such as, what subset of atoms are you using to calculate the entropy? Are you calculating it in dt time frames or are your results cumulative?

Re: [gmx-users] Addition of ions in vacuum simulations

OZGE ENGIN wrote: Hi Mark, I think, it is not a chemistry question exactly. Genion command asks for a group whose atoms are replaced with ions. I have no solvent molecules in my system. In this respect, how can I incorporate ions into my system? use a text editor. Thanks Ozge -Origi

Re: [gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel

> Check out http://wiki.gromacs.org/index.php/Doing_Restarts Thanks very much. I do understand the general restarting mechanism. It is only the first restart that was a little bit confusing > > > I just wanted to confirm if what I am doing makes sense ? Thanks very > > much for the help ! > > T

Re: [gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel

This question is about trying to make sure that I am doing the right thing while trying to use tpbconv to restart jobs. After minimization, for the first dynamics run, I use gen_vel = yes. For subsequent restart runs however, gen_vel must be set to no. After the first dynamics run of 200ps, my

Re: [gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel

himanshu khandelia wrote: Hi This question is about trying to make sure that I am doing the right thing while trying to use tpbconv to restart jobs. Check out http://wiki.gromacs.org/index.php/Doing_Restarts After minimization, for the first dynamics run, I use gen_vel = yes. For subsequent

[gmx-users] GROMETA - Gromacs with Metadynamics, and more

Dear Gromacs users, we have developed a GROMACS release with metadynamics. If your are interested in trying it, you can download it from http://lxmi.mi.infn.it/~provasi/grometa/ If you implement new features in it, we'd like to have them included in our version, too, so let us know! Also let us

[gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel

Hi This question is about trying to make sure that I am doing the right thing while trying to use tpbconv to restart jobs. After minimization, for the first dynamics run, I use gen_vel = yes. For subsequent restart runs however, gen_vel must be set to no. After the first dynamics run of 200ps, my

Re: [gmx-users] qasi-harmonic entropy calculation

Hi, I understand you are using the Schlitter equation, is that so? Could you give more details? Such as, what subset of atoms are you using to calculate the entropy? Are you calculating it in dt time frames or are your results cumulative? Why do you expect the entropy to decrease? Regards, Pedro

[gmx-users] qasi-harmonic entropy calculation

Hi all user, I have calculated entroy over time from eigenvalue(g_covar) and the result shows that the entropy decreasing towards zeo. The results is ok as far as it decreases. But I do not understand why it is approaching to zero towards the end of the simulation. Can anyone explain why? I wo

Re: [gmx-users] Addition of ions in vacuum simulations

What Mark means is that there us little meaning of adding ions in a simulation of a protein in vacuum. There is little sense and use of a simulation of a protein in vacuum, but that could depend on what you are looking for. There is little sense in putting ions in a vacuum environment to neutra

Re: Re: [gmx-users] Addition of ions in vacuum simulations

> Hi Mark, > > I think, it is not a chemistry question exactly. > Genion command asks for a group whose atoms are replaced with ions. > I have no solvent molecules in my system. > In this respect, how can I incorporate ions into my system? Check your assumptions. Does it make sense to put isolated

Re: Re: [gmx-users] Addition of ions in vacuum simulations

Hi Mark, I think, it is not a chemistry question exactly. Genion command asks for a group whose atoms are replaced with ions. I have no solvent molecules in my system. In this respect, how can I incorporate ions into my system? Thanks Ozge -Original Message- From: "Mark Abraham" <[EM