Re: [gmx-users] Unable to view trajectory in pymol or vmd

2008-10-14 Thread vivek sharma
Hi David, Thanks for your response. I was not loading any pdb file. Do I need to do so ? & where ? With Thanks, Vivek 2008/10/14 David van der Spoel <[EMAIL PROTECTED]> > vivek sharma wrote: > >> Hi There, >> >> I have few MD trajectory, I want to analyze them visually (other than ngmx >> option

Re: [gmx-users] Unable to view trajectory in pymol or vmd

2008-10-14 Thread David van der Spoel
vivek sharma wrote: Hi David, Thanks for your response. I was not loading any pdb file. Do I need to do so ? & where ? previous poster just explained in VMD load pdb then load traj.xtc or traj.trr With Thanks, Vivek 2008/10/14 David van der Spoel <[EMAIL PROTECTED]

RE: [gmx-users] Selecting part of the trajectory

2008-10-14 Thread #NGUYEN CONG TRI#
Hi, Thank you very much for your reply. No matter how much I much it backward, even with -b 100 and -e 200 it still doesn't work. And it's not just applied for 1 trajectory, I have 3 others as well but none seems to work. But I'm able to get the snapshots using -dump flag. Of course it's muc

RE: [gmx-users] Unexplained crashes with Gromacs-4.0

2008-10-14 Thread Berk Hess
Hi, I don't really know what could be the problem here. 0..180 is (confusingly) not including the end, so 180 is out of range. The only thing I can think of (except for unknown bugs of coarse), is that I corrected the coupling time of the Parrinello-Rahman barostat when going from 4.0 RC4 to the

Re: [gmx-users] Unexplained crashes with Gromacs-4.0

2008-10-14 Thread Justin A. Lemkul
Berk Hess wrote: Hi, I don't really know what could be the problem here. 0..180 is (confusingly) not including the end, so 180 is out of range. The only thing I can think of (except for unknown bugs of coarse), is that I corrected the coupling time of the Parrinello-Rahman barostat when goin

[gmx-users] Mistake in manpage/manual?

2008-10-14 Thread Christian Seifert
Hi. I think, I found a mistake in the new manual/manpage. Gromacs-4.0 manual(page 279) and manpage for mdrun: "For good load balancing at high parallelization, npme should be divisible by the number of PME nodes." If I got it right, than npme should be the the number of PME nodes. So even for p

Re: [gmx-users] Unexplained crashes with Gromacs-4.0

2008-10-14 Thread David van der Spoel
Justin A. Lemkul wrote: Berk Hess wrote: Hi, I don't really know what could be the problem here. 0..180 is (confusingly) not including the end, so 180 is out of range. The only thing I can think of (except for unknown bugs of coarse), is that I corrected the coupling time of the Parrinello-

[gmx-users] topolbuild 1.2, gromacs topology builder extended to include gromacs united atoms force fields

2008-10-14 Thread Bruce D. Ray
I have submitted a further revision of topolbuild as file topolbuild1_2.tgz Please see the end of this message for an important post-submission code correction. Reads a Tripos .mol2 file with charges to generate something approximating gromacs .gro, .top, and .itp files from it based on selected f

RE: [gmx-users] Mistake in manpage/manual?

2008-10-14 Thread Berk Hess
Hi, This is a bit confusing. npme refers to the number of grid cells in the x and y dimension. You can now use any number. But a high parallelization you will get the best performance when nkx and nky are divisible by npme. Berk > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Date: Tue

Re: [gmx-users] Running MD only for selected part of molecule

2008-10-14 Thread vivek sharma
Hi there, I tried the mdrun by keeping a group of residue position restrained, and it is working well (verified by comparing RMSD plot for the same), thanks for your suggestions regarding the same. But, I have seen that the part of the molecule I kept for PR is still having some motion, how can I

Re: [gmx-users] Octanol

2008-10-14 Thread David van der Spoel
Edson Fauth Vargas Filho wrote: Hello all! I 'm working with a protein and I would like to make a system with octanol. I tried to use the archives that are on line at Gromacs Wiki - User contributions, but this solvent was constructed to OPLS. Then my sistem is very slow. My query is if is th

Re: [gmx-users] How to confine a protein in a box?

2008-10-14 Thread Suman Chakrabarty
Jochen Hub wrote: > Lee Soin wrote: >> Hello, all! I intend to simulate a protein confined in a box. Can anybody >> tell me how to define a boundary, or a wall, in GROMACS? Thanks! > > As far as I know Berk has implemented walls in gromacs 4.0. Check the > new mdp options. Are you sure that you do

[gmx-users] editconf/genbox problem in Gromacs 4.0

2008-10-14 Thread mldaniel
Users, I have recently upgraded from Gromacs3.3 to Gromacs4.0 and I seem to be encountering a problem when trying to solvate a protein in a water box. Editconf command: editconf -bt octahedron -f prot2.pdb -o prot2_test.pdb -c -d 1.0 The output from editconf appears to be normal and the problem

[gmx-users] Hamiltonian replica exchange

2008-10-14 Thread marcos
Hi, Is Hamiltonian replica exchange implemented in gmx 4.0? can't find it in the manual. Marcos. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

Re: [gmx-users] Hamiltonian replica exchange

2008-10-14 Thread David van der Spoel
marcos wrote: Hi, Is Hamiltonian replica exchange implemented in gmx 4.0? can't find it in the manual. No. 4.1 Marcos. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archiv

RE: [gmx-users] Unable to view trajectory in pymol or vmd

2008-10-14 Thread Berk Hess
Hi, Or even simpler, just from the command-line: vmd conf.gro traj.trr or vmd conf.pdb traj.trr Berk Date: Tue, 14 Oct 2008 01:22:40 -0500 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: Re: [gmx-users] Unable to view trajectory in pymol or vmd Hi, In VMD: 1. Load the *.gro file 2.

[gmx-users] Gromacs 4.0 fortran compilation problem solved

2008-10-14 Thread Berk Hess
Hi, When Gromacs 4.0 is compiled with fortran (which one should not do on most platforms since it is not faster, but seems to be the default on for instance an IBM Power6), the compilation would quit with an error of undefined XDR_INT_SIZE in src/gmxlib/libxdrf.c. This has been fixed in CVS for

RE: [gmx-users] Unexplained crashes with Gromacs-4.0

2008-10-14 Thread Berk Hess
> Date: Tue, 14 Oct 2008 07:19:45 -0400 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Unexplained crashes with Gromacs-4.0 > > > > Berk Hess wrote: > > Hi, > > > > I don't really know what could be the problem here. > > > > 0..180 is (confusingly) not inc

[gmx-users] gromacs

2008-10-14 Thread He, Yang
Hi all users, I juse encountered a problem when I run the code about the course grain for DNA, it shows like this creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... calling cpp... In file included from ffyxh.itp:8

Re: [gmx-users] gromacs

2008-10-14 Thread Justin A. Lemkul
He, Yang wrote: Hi all users, I juse encountered a problem when I run the code about the course grain for DNA, it shows like this creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... calling cpp... In file inclu

[gmx-users] (no subject)

2008-10-14 Thread Juliana Angeiras
Hi all,   I'm still having problems with the simple test in the directory rb1. I have used gromacs 3.3.3 and gmxtest 3.3.3. The simple test in the directory simple/rb1/ crashed. The complex test dec+water too, but the problem seems not too serious as the related in the wiki. The configuration a

[gmx-users] gmxtest rb1

2008-10-14 Thread Juliana Angeiras
Hi all,   I'm still having problems with the simple test in the directory rb1. I have used gromacs 3.3.3 and gmxtest 3.3.3. The simple test in the directory simple/rb1/ crashed. The complex test dec+water too, but the problem seems not too serious as the related in the wiki. The configuration a

RE: [gmx-users] gromacs

2008-10-14 Thread He, Yang
Hello Justin, Thank you for your reply. I am using the gromacs to simulate a case about the course grain for DNA. This case includes some superatoms in the course grain force field and I have defined the superatoms in the .atp files and the atoms type in the water like this: Ab 134.1; Adeni

Re: [gmx-users] gromacs

2008-10-14 Thread Justin A. Lemkul
He, Yang wrote: Hello Justin, Thank you for your reply. I am using the gromacs to simulate a case about the course grain for DNA. This case includes some superatoms in the course grain force field and I have defined the superatoms in the .atp files and the atoms type in the water like this:

Re: [gmx-users] gromacs

2008-10-14 Thread Justin A. Lemkul
He, Yang wrote: Hello, This is my content in the *nb.itp [ atomtypes ] ;namemasscharge ptype c6c12 Ab 134.1 0.683A 0.00.0 P1 94.97 -0.276 A 0.00.0 Tb 125.1 -0.683 A0.0 0.0 P2

Re: [gmx-users] Running MD only for selected part of molecule

2008-10-14 Thread Justin A. Lemkul
vivek sharma wrote: 2008/10/14 Justin A. Lemkul <[EMAIL PROTECTED] > vivek sharma wrote: Hi there, I tried the mdrun by keeping a group of residue position restrained, and it is working well (verified by comparing RMSD plot fo

Re: [gmx-users] Running MD only for selected part of molecule

2008-10-14 Thread vivek sharma
2008/10/14 Justin A. Lemkul <[EMAIL PROTECTED]> > > > vivek sharma wrote: > >> Hi there, >> >> I tried the mdrun by keeping a group of residue position restrained, and >> it is working well (verified by comparing RMSD plot for the same), thanks >> for your suggestions regarding the same. >> But, I

[gmx-users] Energy minimisation

2008-10-14 Thread sudheer babu
Hi gmx-users, I am having small doubt on energy minimisation that is I have started protein system, when I do EM its showing that Step size too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 800 Double precision normally gives you higher a

Re: [gmx-users] Unexplained crashes with Gromacs-4.0

2008-10-14 Thread Justin A. Lemkul
David van der Spoel wrote: Justin A. Lemkul wrote: Berk Hess wrote: Hi, I don't really know what could be the problem here. 0..180 is (confusingly) not including the end, so 180 is out of range. The only thing I can think of (except for unknown bugs of coarse), is that I corrected the co

Re: [gmx-users] Running MD only for selected part of molecule

2008-10-14 Thread Justin A. Lemkul
vivek sharma wrote: Hi there, I tried the mdrun by keeping a group of residue position restrained, and it is working well (verified by comparing RMSD plot for the same), thanks for your suggestions regarding the same. But, I have seen that the part of the molecule I kept for PR is still hav

Re: [gmx-users] editconf/genbox problem in Gromacs 4.0

2008-10-14 Thread David van der Spoel
[EMAIL PROTECTED] wrote: Users, I have recently upgraded from Gromacs3.3 to Gromacs4.0 and I seem to be encountering a problem when trying to solvate a protein in a water box. Editconf command: editconf -bt octahedron -f prot2.pdb -o prot2_test.pdb -c -d 1.0 It works for me. Is your input fil

[gmx-users] Octanol

2008-10-14 Thread Edson Fauth Vargas Filho
Hello all! I 'm working with a protein and I would like to make a system with octanol. I tried to use the archives that are on line at Gromacs Wiki - User contributions, but this solvent was constructed to OPLS. Then my sistem is very slow. My query is if is there any MDP, TOP and/or GRO to octano

[gmx-users] density graph

2008-10-14 Thread hhhh huan
Dear all gmx users and developers, Is it correct that in gromacs energy (density graph), the y-axis is labelled as kJ/mol, I am wonder it is not a density unit. Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.o

Re: [gmx-users] density graph

2008-10-14 Thread Justin A. Lemkul
huan wrote: Dear all gmx users and developers, Is it correct that in gromacs energy (density graph), the y-axis is labelledas kJ/mol, I am wonder it is not a density unit. In the output that I have from g_density (v 3.3), the the .xvg file has the y-axis labeled as: yaxis label

Re: [gmx-users] density graph

2008-10-14 Thread hhhh huan
Thanks Justin, I realized my mistake. I get the kj/mol unit because i use g_energy command and select the density option. thanks --- On Wed, 10/15/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > From: Justin A. Lemkul <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] density graph > To: [EMA

[gmx-users] density graph 2

2008-10-14 Thread hhhh huan
Dear all Gmx users and developers, How can i get a density graph with x-axis is time scale? I obtained a density graph using g_density which output a graph with density vs nm (box size). So how can i get a graph with density vs time? Thanks _

[gmx-users] g_lie + running MDS for a ligand only

2008-10-14 Thread vivek sharma
Hi All, I want to use g_lie function of gromacs to calculate the binding free energy og a ligand with the protein. For the same I need to run two MDS, one for ligand only and one for ligand+protein complex (please correct if I am wrong). What are the checks that I should take care in this case, e.