Re: [gmx-users] Distance for window spacing in US?

Hi, As i understand, if pulling geometry is set to 'pull_geometry = distance' and 'pull_dim = Y Y Y" then the DISTANCE between the COM of the enzyme and the ligand is restrained with the umbrella potential. If using long enough simulation times for each restraint umbrella window, as long as the li

[gmx-users] amb2gmx.pl script ignores negative values of PK?

Hi all, There is a problem that I encountered when I was trying to manually verify the proper dihedral conversion from AMBER topology to GROMACS topology using amb2gmx perl script. Some of the dihedrals were set to zero by amb2gmx even if in the prmtop file they were not zero. This was happening f

[gmx-users] mk_angndx

l the dihedrals in the tpr structure file grouped by the force constant of the first Ryckaert-Bellemans coefficient, but I want only the phi-psi dihedrals. Is there a way of doing this? Thanks, Andrei Dr. Andrei Neamtu, PhD, Lecturer Dept. of Physiology "Gr. T.

Re: [gmx-users] free energy landscape question

n 2010, Andrei Neamtu wrote: > >> Dear Andreas and Marc, >> Thanks for your reply. >> I am not familiar with the gromacs programming code and so I am trying >> to build myself the FEL. >> I can generate the hisotgram of the number of states from the >> projecti

Re: [gmx-users] free energy landscape question

Dear Andreas and Marc, Thanks for your reply. I am not familiar with the gromacs programming code and so I am trying to build myself the FEL. I can generate the hisotgram of the number of states from the projection along principal component 1 and 2 (PC1 and PC2) using SigmaPlot but here I am stucke

[gmx-users] free energy landscape question

Hi, I am trying to use g_sham to obtain free energy landscape from a simulation. I can obtain the .xpm files but I want to know if there is any way of obtaining the actual histogram (in a form of a ASCII matrix vith numerical values) to use it in some other plotting program to draw contour lines p

[gmx-users] free energy landscape question

Hi, I am trying to use g_sham to obtain free energy landscape from a simulation. I can obtain the .xpm files but I want to know if there is any way of obtaining the actual histogram (in a form of a ASCII matrix vith numerical values) to use it in some other plotting program to draw contour lines p

Re: [gmx-users] question about compass ff

need to modify the gromacs CODE. Andrei On Wed, Jun 2, 2010 at 2:23 PM, Justin A. Lemkul wrote: > > > Andrei Neamtu wrote: >> >> Dear all, >> >> does anyone know if it is possible to somehow use COMPASS or CVFF >> forcefields in Gromacs? >> > >

[gmx-users] question about compass ff

Dear all, does anyone know if it is possible to somehow use COMPASS or CVFF forcefields in Gromacs? Thanks, Andrei -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Ple

Re: [gmx-users] rmsf question

Hi, thank you all. I have asked the question about RMSD because of the following reason: I simulate a protein whose structure was determined by NMR only. My simulation is quite long (2 microseconds) in the absence of a ligand, present in the experimental structure file. During the course of the s

Re: [gmx-users] rmsf question

! Andrei On Mon, Mar 15, 2010 at 10:00 AM, Mark Abraham wrote: > On 15/03/2010 6:45 PM, Andrei Neamtu wrote: >> >> Dear Mark, >> >> Thank you very much for your response. >> >> What I meant was to obtain a RMSF plot form PDB mediated on each >> residue and

Re: [gmx-users] rmsf question

x. And also the same number of atoms in the corresponding residues.) Many thanks, Andrei On Sun, Mar 14, 2010 at 3:16 PM, Mark Abraham wrote: > On 14/03/2010 7:47 PM, Andrei Neamtu wrote: >> >> Hi, >> >> is there a rapid way to compute RMSF on an NMR ensemble from a

[gmx-users] rmsf question

Hi, is there a rapid way to compute RMSF on an NMR ensemble from a PDB file? g_rmsf needs a .tpr file. This is OK with the MD trajectories but if I want to compare MD ensemble one with the NMR RMSF ensemble fluctuations from the original PDB this is not possible. Thanks, Andrei -- gmx-users mai

[gmx-users] periodic moleules

Hi, I am trying to build a hydrogel polymeric system and I want to make use of the option periodic_molecules. In this regard I am a little bit confused. are there any other keywords except the option 'peridic molecules' that I have to set to define a periodic polymer chain e.g. in the molecula

Re: [gmx-users] g_order warning message

n Wed, Aug 5, 2009 at 1:43 PM, Justin A. Lemkul wrote: > > > Andrei Neamtu wrote: >> >> Hello, >> >> I am trying to use g_order (gmx 4.0.5) on a coarse grained membrane. >> Because the distances between two atoms two bonds apart is greate

[gmx-users] g_order warning message

Hello, I am trying to use g_order (gmx 4.0.5) on a coarse grained membrane. Because the distances between two atoms two bonds apart is greater than 0.3nm I keep receiving the message: . Warming: distance between atoms * and X > 0.3 nm (**) . Index f

[gmx-users] PME nodes

Hello, How can I compile the g_tune_pme program available at: http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/ Many thanks, Andrei ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinf

[gmx-users] pull code problem solved..

Sorry it appears that something was wrong with my .mdp file .. Idon't know what ...but I wrote again the pull code lines and the warnings dissapeared. Thank you again, Andrei ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mail

[gmx-users] pull code problem

Hi Berk, thank you for the reply here is my mdp file: ; ; User aneamtu ; Joi, 7 mai - 2009 ; Input file ; title = Production_runs ;define = -DPOSRES -DPOSRES_CA2+_IONS ;constraints = all-bonds integrator =

[gmx-users] pull code problem

hello, I am trying to do a pulling simulation with gromacs 4.0.2 I added the following lines to the .mdp input file for grompp: ... pull = constraint pull_geometry = distance pull_dim = Y Y Y pull_nstxout = 10 pull_nstfout = 10

[gmx-users] Re: Martini Cg-model can not be downloaded!

Which browser do you us? I had the same problem with Internet explorer. Try Firefox! Andrei ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search be

Re: [gmx-users] Martini Cg-model can not be downloaded!

I had the same problem with Internet explorer. Try Firefox! Andrei On Tue, Feb 10, 2009 at 9:41 AM, xi zhao wrote: > well.. it seems that there is a problem in the page for downloading files > from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html, the cg model > parameters can not be downlo

Re: [gmx-users] PBC only in xy direction

Hi, How is it possible a vacuum layer be maintained without solvent evaporation? (in absence of few solvent layers positionally restrained or in absence of walls which work only in pbc=xy) Andrei (maybe the question is trivial but I cannot figure out the answer) On Thu, Dec 11, 2008 at 11:50 AM

Re: [gmx-users] error while compiling gromacs 4.0.2

try to add in your .bashrc this export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/openmpi-1.2.8/lib or whatever your mpi lib directory is Andrei On Thu, Dec 4, 2008 at 12:08 PM, Ragothaman Yennamalli <[EMAIL PROTECTED]> wrote: > Dear all, > While compiling gromacs 4.0.2 in a AMD 64bit dual pr

[gmx-users] test particle insertion

Hello, Where can be found more information on test particle insertion method as implemented in gromacs? It is possible to use molecules as test particles? Thank you a lot, Andrei ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

Re: [gmx-users] problem with npt

Hi, have you checked if there is no water inside the membrane after the use of genbox? On Dec 16, 2007 1:35 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > pragya chohan wrote: > > > > i started with the lipid coordinates from peter tieleman and removed the > > water. then i added water by genbox. >

[gmx-users] make hole question

Hello gmx, I have a quick question: with what distribution of gromacs the mdrun make hole works? Cu bine, Andrei ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://w

[gmx-users] infiniband question

Hello gmx, I have a question regarding infiniband interconnect: Is there any difference (in terms of performance) between integrated on-board infiniband (ex. Mellanox) and PCI-Express infiniband adaptors (due to pci-e limitations)? Which one is recomended. We are in a process of buying a cluster o

[gmx-users] re:multi problem

Thanks a lot Mark and Ye, I will try both alternatives! Andrei ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don'

[gmx-users] re:multi problem again

Dear Mark, Thank you for your reply! I thought that maybe the accessibility were the problem. I don't figure how to set the working directory of say node 1 to my current working directory on node 0. I setup node 1 to be able to access node 0 through ssh with no password but the problem rem

[gmx-users] multi problem

Dear gmx users, I have problems in running a simulation on several nodes using the -multi option: I make the .tpr files for different temperatures (I want to use the REMD code) grompp -f param0.mdp -po param0.out.mdp -c conf.gro -p topol.top -o sim0.tpr grompp -f param1.mdp -po param1.out.m

[gmx-users] performance question

Hello, We are in the process of building a cluster on which GROMACS will be the main computational engine and I have a question about performance. We are not yet decided what to buy (we can not test them in advance). Which configuration do you think will be better: - 8 servers with 2 x dual