Re: [gmx-users] Gromacs inquiries

Dear Mark, I used to put ten molecules of hexanol in a box 5 5 1 with the instruction "genbox -ci hexanol.gro -nmol 10 -box 5 5 1 -o layer.gro -p hexanol.top". However, now I want to fill up the box 4 4 4 with hexanol molecules. If I change the number 10 in the instruction to 1000 or 1, it wil

Re: [gmx-users] Gromacs inquiries

On 26/10/2011 1:46 PM, cuong nguyen wrote: Dear, Thanks a lot for useful software. I am trying to generate a box (4 4 4) with full hexanol molecules inside. I have used the instruction "genbox -ci hexanol.GRO -box 4 4 4 -o layer.gro -p hexanol.top", however it has not been successful. Unfor

[gmx-users] Gromacs inquiries

Dear, Thanks a lot for useful software. I am trying to generate a box (4 4 4) with full hexanol molecules inside. I have used the instruction "genbox -ci hexanol.GRO -box 4 4 4 -o layer.gro -p hexanol.top", however it has not been successful. Please correct the instruction for me or give me any ad

Re: [gmx-users] Fatal error in MPI_Allreduce upon REMD restart

On 26/10/2011 6:06 AM, Szilárd Páll wrote: Hi, Firstly, you're not using the latest version and there might have been a fix for your issue in the 4.5.5 patch release. There was a bug in 4.5.5 that was not present in 4.5.4 that could have produced such symptoms, but it was fixed without creati

Re: Re: [gmx-users] failure during compiling gromacs 4.5.5

Hi, > Thank you very much. I removed -xHOST from CFLAGS and FFLAGS, and now it > runs correctly. Good that it worked. Still it's bizarre that icc failed at compiling the code it generated... FYI: removing the flag might result in slightly slower binaries, but the difference should be quite small

Re: [gmx-users] Fatal error in MPI_Allreduce upon REMD restart

Hi, Firstly, you're not using the latest version and there might have been a fix for your issue in the 4.5.5 patch release. Secondly, you should check the http://redmine.gromacs.org bugtracker to see what bugs have been fixed in 4.5.5 (ideally the target version should tell). You can also just do

Re: [gmx-users] nonane solvent

Vijayaraj wrote: Hello, I need to simulate a peptide in nonane solvent environment using ff99SB force field. As there are different procedures used to create a solvent box, different from water, specific to several force fields, I would like to make sure the method which I am going to use w

[gmx-users] Fatal error in MPI_Allreduce upon REMD restart

Hi all, I'm getting errors in MPI_Allreduce what I restart an REMD simulation. It has occurred every time I have attempted an REMD restart. I'm posting here to check there's not something obviously wrong with the way I'm doing the restart which is causing it. I restart an REMD run using: --

[gmx-users] nonane solvent

Hello, I need to simulate a peptide in nonane solvent environment using ff99SB force field. As there are different procedures used to create a solvent box, different from water, specific to several force fields, I would like to make sure the method which I am going to use will be appropriate for m

Re: [gmx-users] Simulation of membrane protein

James Starlight wrote: Justin, I've found the same task of MSU's students :) They simulate membrane formation without NPT stage ( after NVT they run production MD). From they reports I've found that simplest membrane system could be formed within 10-30 Ns. But what about try to make such s

Re: [gmx-users] Simulation of membrane protein

Hey James, > I've found the same task of MSU's students :) They simulate membrane > formation without NPT stage ( after NVT they run production MD). From they > reports I've found that simplest membrane system could be formed within > 10-30 Ns.  But what about try to make such simulation in vacuum

Re: [gmx-users] Simulation of membrane protein

Justin, I've found the same task of MSU's students :) They simulate membrane formation without NPT stage ( after NVT they run production MD). From they reports I've found that simplest membrane system could be formed within 10-30 Ns. But what about try to make such simulation in vacuum at first w

Re: [gmx-users] Simulation of membrane protein

James Starlight wrote: Justin, Could you tell me if I want to simulate self-organization of the pure lipid bilayer starting from the initial random placed molecules in water. Does this simulation need in pre-md NVT and NPT equilibration? Some form of equilibration is always required. Wha

Re: [gmx-users] Lyzosyme with ligand tutorial

On 25/10/2011 5:29 PM, James Starlight wrote: This was due to that in .gro file corresponded to the end of productive MD I've found this http://i1209.photobucket.com/albums/cc394/own11/mdL.png It's looks like the protein moved out from box so I've thought that some error occured during stimul

[gmx-users] the order parameter obtained by g_angle

Dear all, Who can tell me how the order parameter obtained by g_angle is defined? or where can I find the details? Thanks very much. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] Simulation of membrane protein

Justin, Could you tell me if I want to simulate self-organization of the pure lipid bilayer starting from the initial random placed molecules in water. Does this simulation need in pre-md NVT and NPT equilibration? What the average time for NPT? I think that If this stage should occur it must be c