[gmx-users] density map in 3 Dimension

Dear gromacs-users,  I thought of sending this query again as I did not get any response in my last email.   I was wondering whether there is any way to calculate the 3D density map of a particular selection of protein-water system ( say the water near the protein backbone) in gromacs. I guess g

[gmx-users] 3D density Map

Dear Gromacs users,   I was wondering whether there is any way to calculate the 3D density map of a particular selection of protein-water system ( say the water near the protein backbone) in gromacs. I guess g_densmap provides a 2D map of the density. But I was looking for 3D map of density. I

[gmx-users] problem with replica exchange

Hi,  I am having a problem in running replica exchange simulation over multiple nodes. To run the simulation for 16 replicas over two 8-core processors, I generated a hostfile as follows: yethiraj30 slots=8 max_slots=8  yethiraj31 slots=8 max_slots=8 These two machines are intra-connected and I

[gmx-users] molecular surface area(MSA)?

Hi,  I was wondering whether gromacs can calculate a quantity called molecular surface area(MSA) which is different from solvent accessible surface area(SASA). By definition, SASA of a molecule is the area of surface traced by center of a spherical water probe rolling on a vander wall surface of

Re: [gmx-users] problem with energy groups and mdrun -rerun option

: From: Justin A. Lemkul Subject: Re: [gmx-users] problem with energy groups and mdrun -rerun option To: "Discussion list for GROMACS users" Date: Friday, 22 October, 2010, 2:56 AM jagannath mondal wrote: > Hi, >   I have  used gromacs 4.0.7 to do  MD simulation of two solutes

[gmx-users] problem with energy groups and mdrun -rerun option

Hi,  I have  used gromacs 4.0.7 to do  MD simulation of two solutes A & B in water ( solvent) . Initially, I had set "energy groups = system " and used mdrun to do the simulation. Now,I wanted to get the potential energy contribution from due to interaction of  A-A, B-B,A-B A-solvent, B-solvent,

Re: [gmx-users] problem with g_clustsize

Thanks. Just wondering what is a 'distal atom' as you mentioned.   I am creating a new subject on g_clustsize.  --- On Wed, 7/7/10, chris.ne...@utoronto.ca wrote: From: chris.ne...@utoronto.ca Subject: [gmx-users] problem with trjconv -pbc cluster To: gmx-users@gromacs.org Date: Wednesday, 7 Ju

Re: [gmx-users] problem with trjconv -pbc cluster

Hi Chris,  Thanks a lot for your responses. I will surely try them. But, before I go to trjconv -pbc cluster, I had one more problem to sort out. This has to do with quantifying the cluster-size distribution from the trajectory. As I mentioned, if I visualize the trajectory in VMD, I see that st

Re: [gmx-users] problem with trjconv -pbc cluster

the program is in an infinte loop.  Jagannath  --- On Wed, 7/7/10, Mark Abraham wrote: From: Mark Abraham Subject: Re: [gmx-users] problem with trjconv -pbc cluster To: "Discussion list for GROMACS users" Date: Wednesday, 7 July, 2010, 12:20 PM - Original Message ----- From:

[gmx-users] problem with trjconv -pbc cluster

Hi,  I had a system of surfectants which are started with an initial configuration where all of them are well dispersed. Visual study of trajectory shows they start aggregating and finally form two discrete micelles. To quantify this micelle clusterization, I tried to use the suggestions present

[gmx-users] fftw library problem in gromacs installation

Hi ,  I am having a problem in installing gromacs-4  in a suse linux in a powerpc ibm machine. The problem is that  1.  I first  installed fftw in the following way :for single precision./configure --enable-float --enable-threads --prefix=/N/u/tg-jmondal/BigRed/UTIL/fftwmakemake install Then for

Re: [gmx-users] g_angle between center of mass of three groups

t for GROMACS users" Date: Wednesday, 4 November, 2009, 9:00 AM jagannath mondal wrote: > Hi, > >   I know that g_dist gives the distance between the center of masses of  two >groups.  But, I wanted to know whether it is possible to calculate angle >between center of masses of t

[gmx-users] g_angle between center of mass of three groups

Hi,   I know that g_dist gives the distance between the center of masses of  two groups.  But, I wanted to know whether it is possible to calculate angle between center of masses of three groups or not . I am not sure whether g_angle can calculate the angle between center of masses of three gro

[gmx-users] How to get centre of mass bond & angle distribution

Hi,   I am trying to coarse-grain a system. For that I want to optimize the bond , angle and dihedral parameters of coarse-grained model based on atomistic simulation. For that, in the atomistic simulation part, I want to calculate the the distribution of 'effective' angle made by the 'centre of

[gmx-users] comparison of gromacs in CENTOS and UBUNTU

Hi,   I was planning to install one of the linux distributions : CENTOS or UBUNTU in our xeon 8-core processor.  Can any one suggest which one will be better for Gromacs as far as installation and performance is concerned?ThanksJagannath Love Cricket? Check out live scores, photos, video

[gmx-users] gromacs-3.3.1 tpr file in gromacs 4.0.5?

Hi,  I was wondering whether one can use a .tpr file  made using gromacs-3.3.1 in gromacs 4.0.5 to restart or exactly continue a simulation or not.ThanksJagannath Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/_

[gmx-users] mpi problem

Hi,I am trying to use parallel gromacs3.3.3  mdrun programme  .I have installed mpich2 in our quadcore machine. But I am having 3 problems:   1. The scaling is very poor among 4 cores: varies between 30-70 %.    2. If I run the mdrun_mpi in background, the output log file cites following error: 

[gmx-users] problem with mpi

Hi,I am trying to use parallel gromacs3.3.3  mdrun programme  .I have installed mpich2 in our quadcore machine. But I am having 3 problems:   1. The scaling is very poor among 4 cores: varies between 30-70 %.    2. If I run the mdrun_mpi in background, the output log file cites following error: 

[gmx-users] implicit solvent in gromacs 4.0?

Hi, I was curious to know whether gromacs 4.0 supports implicit solvent simulation or not. If not, is there any possibility that the implicit solvent model will be implemented in near future ? Thanks Jagannath Mondal Send free SMS to your Friends on Mobile from your Yahoo! Messenger

[gmx-users] problem with structure factor in g_rdf

Hi, I was trying to use g_rdf analysis tool to calculate the structure factor of a polymer I am simulating. I have generated own ..itp files for the polymer and the simulation is going ok. But, whenever, I am trying to use g_rdf tool to calculate the structure factor, it returns the followi

[gmx-users] query regarding self-assembly process

Dear gromacs users, I am trying simulate self-assembly of protein on gold surface. To get an idea, I was looking for various literatures which this kind of self-assembly. Many of them reports that they used periodic boundary condition in X and Y diection(gold-surface is in one extreme of z dir

[gmx-users] request for help to prepare a 111 gold surface

other programme to generate the 111 surface. . Thanks in advance, Jagannath Mondal Download prohibited? No problem! To chat from any browser without download, Click Here: http://in.messenger.yahoo.com/webmessengerpromo.php ___ gmx-users

RE: [gmx-users] problem with freeze-group : Large VCM(Berk Hess)

I am again giving the .mdp file. --- Berk Hess <[EMAIL PROTECTED]> wrote: > > > > >From: jagannath mondal <[EMAIL PROTECTED]> > >Reply-To: Discussion list for GROMACS users > > >To: gmx-users@gromacs.org > >Subject: [gmx-users] problem with freeze-gr

Re: [gmx-users] query regarding a topology file

Thanks for reply. Yes, it uses the force-field file I created. Basically I found out that the dihedral which the program skips is also 0. On Apr 12, 2007, at 8:43 PM, Dallas B. Warren wrote: Can't really help you directly, but it comes to mind when I read that error that may be something is

Re: [gmx-users] what are the options for implicit solvent in Gromacs?

: Jagannath Mondal wrote: Hi, I am trying to learn how to use implicit solvent model for PMF calculation. For that ,I wanted to know what are the options for implicit solvent present in gromacs. But I could not find any documentation regarding that. I searched mailing list and found that

[gmx-users] what are the options for implicit solvent in Gromacs?

other options for Generalized Born model? Thanks in advance,, Yours sincerely, Jagannath Mondal ___ gmx-users mailing list[EMAIL PROTECTED] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] query regarding a topology file

pe it used to give an warning for not showing that, But In this case, it is skipping some dihedral types though they are present in the ff***bon.itp file. Can you say whether this is a serious error or it is OK? Thanks, Jagannath Mondal ___

[gmx-users] query regarding topology file

has got 0 initial velocity and during simulation it gains a random velocity ? Yours sincerely Jagannath Mondal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Query regarding PDB2gmx

n toplgy files? Thanks. Jagannath MOndal ___ 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't post (un)sub

Re: [gmx-users] query about making a pdb file

, Jay Mashl wrote: PyMOL (http://pymol.sf.net) is one option for building the chain based on natural amino acids and subsequently performing mutations. Jay On Wed, 28 Mar 2007, Jagannath Mondal wrote: Date: Wed, 28 Mar 2007 23:54:27 -0500 From: Jagannath Mondal <[EMAIL PROTECTED]> Re

[gmx-users] query about making a pdb file

generate the cartesian coordinates of the molecule. At least, can you suggest some software which are free and have mac- version so that I can generate the coresponding PDB file of the molecule from the cartesian coordinates. Thanks, Jagannath Mondal