Re: [gmx-users] Initial cell size is smaller than the cell size limit..

On 7/22/13 1:20 AM, Kavyashree M wrote: Dear users, While running a ligand bound MD using AMber03 force field. I got the following error after ~ 4.9 ns The initial cell size (1.247705) is smaller than the cell size limit (1.586683), change options -dd, -rdd or -rcon, see the log file for detai

Re: [gmx-users] Persistence length calculation using g_polystat

Which group of atoms you have taken for the persistence length? g_polystat requires a group of atoms which are consecutively bonded in polymer main-chain. You should take only backbone atoms of one strand of the DNA. But, it does not give the persistence length for the whole DNA. I guess, to estima

[gmx-users] Calculate interaction energy dynamically

Dear Gromacs Users, Is there a way in Gromacs to calculate the interaction energy between any two neighbor lipids dynamically? Since the neighbor lipids change over time in the trajectory file specifying a static energy groups in the input script will not help. Is there a way to accomplish thi

Re: [gmx-users] Compilation problem with Gromacs 4.5.7 (autoconf only)

I've got the same error. Uninstall automake 1.11 and install automake 1.10 For me it solved the problem. Luís On 20 July 2013 12:42, Suman Chakrabarty wrote: > Hello, > > I am not sure whether this is a known problem, but it seems > gromacs-4.5.7 compilation using autoconf tool is still broken

Re: [gmx-users] Persistence length calculation using g_polystat

Hello Sir, Thank you very much for a reply. I have selected following atoms P, C5',C4',C3' atoms to estimate persistence length. I want to find persistence length of whole dna, can you please elaborate on , how to calculate persistence length of whole dna using helical axis of the

Aw: [gmx-users] Calculate interaction energy dynamically

  You still might be able to with a static group, such that you pick 5 random ones, then the rest as a block (all lipids).  Your only problem may be if you define say 5 of 100 independent, then you would have to sum A-B plus A-all others, so more complicated, but its just a suggestion.   Stephan

Re: [gmx-users] Calculate interaction energy dynamically

On 7/22/13 6:20 AM, Davit Hakobyan wrote: Dear Gromacs Users, Is there a way in Gromacs to calculate the interaction energy between any two neighbor lipids dynamically? Since the neighbor lipids change over time in the trajectory file specifying a static energy groups in the input script wil

RE: [gmx-users] Calculate interaction energy dynamically

Thanks very much for all your suggestions! > One way that you might approach it is to use mdrun -rerun. You could order > the > lipids with respect to the lipid of interest, such that the reference lipid > is > always molecule N and the nearest lipid is always written as N+1 in the > ordered

Re: [gmx-users] Calculate interaction energy dynamically

On 7/22/13 8:37 AM, Davit Hakobyan wrote: Thanks very much for all your suggestions! One way that you might approach it is to use mdrun -rerun. You could order the lipids with respect to the lipid of interest, such that the reference lipid is always molecule N and the nearest lipid is always

Re: [gmx-users] Re: Problem with Amber99SB-ILDN ff

Hi I can't see which commands you typed. Your second try "/bin/sh: 1: -i: not found" means that you $PATH is not properly setup for Amber Tools. And if you using open babel, it has to be your $PATH as well. For the first case, it's all about which structure you were trying to run. >From the pdbs

[gmx-users] Re: Problem with Amber99SB-ILDN ff

Hi, This is more or less that I was thinking after look carefully all the errors. Thank you for your answer and your time. Melchor S. -- View this message in context: http://gromacs.5086.x6.nabble.com/Problem-with-Amber99SB-ILDN-ff-tp5009641p5010029.html Sent from the GROMACS Users Forum ma

Re: [gmx-users] LAMBADA and InflateGRO2

Hi Atila, Lambada was not able to properly identify the membrane reference atoms and you get that error message when it tries to calculate the membrane centre in the Z-axis. Although I'm not an expert I would recommend you to use an index file for the protein and the membrane (options -n1 and -n2

[gmx-users] Simulating a semi-membrane protein

Dear Users, I'm not sure if the term I coined as semi-membrane protein is correct. But My protein is half (alpha subunit) in membrane and other half (beta subunit) outside the cell. is it possible to simulate such proteins? if So, how can we use membrane for just one half? Sorry if the question is

Re: [gmx-users] Simulating a semi-membrane protein

On 7/22/13 9:13 PM, pavithrakb wrote: Dear Users, I'm not sure if the term I coined as semi-membrane protein is correct. Either a protein is a membrane protein or it is not. Is any part of it embedded or bound to the membrane? If yes, it is a membrane protein. But My protein is half (al

Re: [gmx-users] Multi-level parallelization: MPI + OpenMP

Dear Szilárd, I'm making some tests using 2 ranks/node, what I was trying to do. It seems working now, thank you. Éric. On 07/19/2013 08:56 PM, Szilárd Páll wrote: Depending on the level of parallelization (number of nodes and number of particles/core) you may want to try: - 2 ranks/

[gmx-users] Re: Simulating a semi-membrane protein

Dear Sir, Thank you. I understand it now. But, when apply the force field, should I select the membrane ff like gromos56 (like in your KALP tutorial) or will it be a complex process to select a ff? -- View this message in context: http://gromacs.5086.x6.nabble.com/Simulating-a-semi-membrane-pr

[gmx-users] Re: Simulating a semi-membrane protein

Dear Sir, Thank you. I understand it now. But, when apply the force field, should I select the membrane ff like gromos56 (like in your KALP tutorial) or will it be a complex process to select a ff? -- View this message in context: http://gromacs.5086.x6.nabble.com/Simulating-a-semi-membrane-pr