[gmx-users] Questions on combination of Berger's united-atom force field for lipid and OPLS_AA force field for protein

Your first question is addressed in the following document: http://www.pomeslab.com/files/lipidCombinationRules.pdf Your second and third question are addressed (in general form) in the gromacs manual. If you want a topology file, send me a personal email indicating the lipid that you are

Re: [gmx-users] index file groups

> > Thank you Mark for your detailed explanation. Sorry if I am slow in >> understanding some stuff. I appreciate your patience. >> >> 1- I have an inquiry about index groups. If I specify all my solute chains >> as a whole in one group [all chains] (including n chains having m atoms >> each) and c

Re: [gmx-users] GAUSSIAN Error message

  On February 25, 2011 at 1:14 AM Txema Mercero wrote: > >  # HF/6-31G OPT FREQ ^M ^M ARGUSLAB-GENERAT > > Could be related to the ^M ^M characters? This sometimes happens when > you transfer files form windows to linux. > You may try

Re: [gmx-users] PBC

Thank you Justin, indeed it's pbc = xyz in my md.log file. Carla On Fri, Feb 25, 2011 at 3:20 PM, Justin A. Lemkul wrote: > > > Carla Jamous wrote: > >> Hi everyone, >> >> In my .mdp MD file, I didn't put "pbc =xyz". Then, I used tpbconv and >> mdrun to continue my simulation. >> >> My questio

Re: [gmx-users] PBC

Carla Jamous wrote: Hi everyone, In my .mdp MD file, I didn't put "pbc =xyz". Then, I used tpbconv and mdrun to continue my simulation. My question is: did I run my simulation using periodic boundary conditions because I have the impression that I did but I'm not sure if not using the men

[gmx-users] Values of radial density profiles

Dear All I would like to compute the radial density function rho(r) (in g/cm3) of different parts of micelle formed with DPC molecules (such as headgroup, alkyl tail and water) relative to the center of mass of the aggregate. I have constructed an index files containing all the atoms of the surf

[gmx-users] PBC

Hi everyone, In my .mdp MD file, I didn't put "pbc =xyz". Then, I used tpbconv and mdrun to continue my simulation. My question is: did I run my simulation using periodic boundary conditions because I have the impression that I did but I'm not sure if not using the mention "pbc" in my mdp file m

[gmx-users] Questions on combination of Berger's united-atom force field for lipid and OPLS_AA force field for protein

Dear All: I am using GROMACS package to simulate membrane proteins. I plan to use Berger's united atom force field (Berger's UA FF) for lipids and OPLS_AA force field (OPLS_AA FF) for proteins. I have read the guide post kindly by Prof. Dr. Chris Neale in previous mailing lists very caref

Re: [gmx-users] Performance in ia64 and x86_64

Carsten Kutzner wrote: > With Fortran kernels I got a performance of 0.31 ns/day for an 80,000 atom >system > (with PME) on an Altix 4700, so your 0.5 ns/day for 1,500 waters seems too > slow >to me. > What processor is this? Are you shure you are using the Fortran and not the C >kernels? I

Re: [gmx-users] how many contacts has a certain atom at MD

Olga Ivchenko wrote: Thank you Justin, Because the pressure is how often molecules collide with each other, what has a relation to number of contacts between two molecules. Clearly, but do you have any real data that suggest (based on pressure or anything else) that explains the non-differ

Re: [gmx-users] how many contacts has a certain atom at MD

Olga Ivchenko wrote: Regarding my previous question. I performed 2 simulations (minimization, NVT, NPT, and that 10ns production run), one with 300K and another with 309K. Fir each temperature I calculated how many contacts has my molecule with water within a certain distance. But the number

Re: [gmx-users] index file groups

On 25/02/2011 6:37 PM, Nick wrote: Hello to all, Please help me with the following questions. Your attention is greatly appreciated. 1- I have an inquiry about index groups. If I specify all my solute chains as a whole in one group [all chains] (including n chains having m atoms each) and c

Re: [gmx-users] Performance in ia64 and x86_64

On 25/02/2011 8:25 PM, Ignacio Fernández Galván wrote: I wrote: It seems the x86_64 processor has 4 cores and 8 threads support (), so the machine has probably two physical processors. I thought MPI was only needed if there was network communication

Re: [gmx-users] how many contacts has a certain atom at MD

Regarding my previous question. I performed 2 simulations (minimization, NVT, NPT, and that 10ns production run), one with 300K and another with 309K. Fir each temperature I calculated how many contacts has my molecule with water within a certain distance. But the number of contacts at different te

Re: [gmx-users] Performance in ia64 and x86_64

Hello Ignacio, On Feb 25, 2011, at 10:25 AM, Ignacio Fernández Galván wrote: > Well, I've compiled mdrun with MPI (with fortran kernels in the ia64), and > run > my test system in both machines, with a single processor. The results are > still > worrying (to me). This is a 50 time step (0.

Re: [gmx-users] Performance in ia64 and x86_64

I wrote: > It seems the x86_64 processor has 4 cores and 8 threads support > (), so the machine has probably > two > > physical processors. I thought MPI was only needed if there was network > communication involved, as in a cluster, but not in SMP,

Re: [gmx-users] GAUSSIAN Error message

> # HF/6-31G OPT FREQ ^M ^M ARGUSLAB-GENERAT Could be related to the ^M ^M characters? This sometimes happens when you transfer files form windows to linux. You may try "dos2unix" On Thu, Feb 24, 2011 at 8:07 PM, Sergio Manzetti wrote: > No. It contains a charged Gandolinium ion in the middle o