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

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 (at least for me). The ./configure step completes without any error. But "make" fails with the following error regarding not finding certain version of aclocal and autom

[gmx-users] Setting attractive part (C6 parameter) zero in non-bonded parameters

Hello, Following the Section 5.3.2 of the manual, I have tried to set the C6 term of the non-bonded (Lennard-Jones) interaction to zero as follows: "When sigma and epsilon need to be supplied (rules 2 and 3), it would seem it is impossible to have a non-zero C12 combined with a zero C6 paramete

[gmx-users] Temperature in Brownian Dynamics simulation

-grps = Protein ref_t = 300 Pcoupl = no gen_vel = yes gen_temp= 300 gen_seed= 173529 = Please help me troubleshoot this problem. Thanks. Best regards, Suman Chakrabarty

Re: [gmx-users] Temperature in Brownian Dynamics simulation

On Fri, Apr 17, 2009 at 5:32 AM, Mark Abraham wrote: > Suman Chakrabarty wrote: >> >> Hi, >> >> it was pointed out before that for Brownian Dynamics simulation, the >> temperature calculated by g_energy does not match with the ref_t in >> paramete

Re: [gmx-users] Temperature in Brownian Dynamics simulation

. If one has to use a general thermostat indeed, then please advise which thermostat would be best appropriate for BD/SD simulations. Thanks, Suman. On Fri, Apr 17, 2009 at 4:55 PM, Suman Chakrabarty wrote: > On Fri, Apr 17, 2009 at 5:32 AM, Mark Abraham wrote: >> Suman Chakrabarty wr

Re: [gmx-users] Temperature in Brownian Dynamics simulation

archives). > > http://www.gromacs.org/pipermail/gmx-users/2007-July/028379.html > > -Justin > > Suman Chakrabarty wrote: >> >> Dear developers, >> >> could any of you please confirm whether one has to use certain general >> thermostat in brownian dynami

[gmx-users] problem with particle decomposition in gromacs 4.0.4

Hi, I am trying particle decomposition with gromacs 4.0.4 for a small polymer (20 atoms) in SPC/E water. Unfortunately every run crashes at the very beginning without any useful error message, when I use version 4.0.4 with option -pd. Whereas everything remaining same it's still running fine in ve

RE: [gmx-users] problem with particle decomposition in gromacs 4.0.4

Yes, I have encountered this crash with plain Gromacs 4.0.4 as well. I have not tried single processor, but with domain decomposition it runs fine. I am not sure whether it has got to do anything with our parallel architecture though. In any case, I shall file a report after I reproduce this f

[gmx-users] Ryckaert-Bellemans type dihedral

Hi, I need to write my own topology file for a system using Ryckaert-Bellemans type dihedral potential. Since I should remove the 1-4 non-bonded interaction in this case, I wanted to know whether it is enough not to keep any [ pairs ] entry in the topology file (manual page 113), or I should expli

[gmx-users] structure factor using g_rdf: grid option does not work

Hi, I was trying to get the static structure factor using the following command line: g_rdf -f -s -sq -b 15000 -e 2 -endq 0.5 The output sq.xvg came as follows: 0.0 0.0 0.0861717775.32914 0.1723317292.77243 0.2585016632.64157 0.3446615728.30566

[gmx-users] Generating solvent topology using pdb2gmx

Hi, I am trying to generate the topology file for a system containing a single polymer chain in pure DMSO. I have successfully generated the system configuration using genbox. But when I run pdb2gmx on it to create the topology file using the G53a6 force field, it treats the whole system as a sing

[gmx-users] Questions about g_sham options

the X-axis ranges from 0 to 30! What is contained in this file? What am I doing wrong? What would be the right way to generate the free energy surface for both 1- and 2-dimensional cases? Thanks. Regards, Suman Chakrabarty. ___ gmx-users mailing list

Re: [gmx-users] Questions about g_sham options

On Wed, Sep 2, 2009 at 9:08 PM, David van der Spoel wrote: > Suman Chakrabarty wrote: > >> Hi, I have been trying to use the g_sham tool to generate a histogram/free >> energy profile. Unfortunately a few of the output options are not explained >> in the manual or &quo

[gmx-users] angle dependent rdf

According to the manual "With g_rdf it is also possible to calculate an angle dependent rdf g_{AB}(r, \theta)". But I could not find any such specific option from "g_rdf -h". Has it been actually implemented yet? Regards, Suman. ___ gmx-users mailing l

Re: [gmx-users] Simulation of a protein confined in a box

Possibly what he is interested in is a system WITHOUT PBC? I don't think with PBC the system is really "confined", since there is no true wall to reflect the colliding molecules. Thus to study the effect of real confinement, it is necessary to remove PBC and impose reflective boundary conditions. I

Re: [gmx-users] Opinion: Can position restraining waters increase the speed of the md simulation?

On a related note, I remember reading a paper recently, where they take a few shells of water molecules with full atomicity, but "continuum" beyond that. They also took care about the exchange between the "molecular" water shell and the continuum as the polymer/protein conformation changes during t

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

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

Re: [gmx-users] stochastic dynamics , langevin

Berk Hess wrote: > Everything depends on what you want to do, which you do not tell in detail. > If you want to leave out the solvent, but you want to simulate a system > in solvent, > SD is not going to help you, since there is no implicit solvent potential, > so your potential and therefore your

Re: [gmx-users] Gromacs-4.0.2 is out

Great job! Around when will the manual be ready? Regards, Suman Chakrabarty. Erik Lindahl wrote: > Hi, > > I think we've fixed all minor issues with Gromacs-4.0 now; please > download the new release from > > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.0.2.tar.gz &

Re: [gmx-users] GROMACS on Bluegene

I am interested in this as well, since I am planning to compile version 4.0.2 in Blue Gene within a few days (once I get hold of my account!). -- Suman Chakrabarty. On Wed, Nov 12, 2008 at 8:21 PM, Mike Hanby <[EMAIL PROTECTED]> wrote: > Has there been any further discussion about f

[gmx-users] GROMOS with SPC/E water?

ure I am using SPC/E water, while genbox uses the default spc216.gro? Regards, -- Suman Chakrabarty -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-us

Re: [gmx-users] GROMOS with SPC/E water?

guration file (to be used with genbox) same for both spc and spce? >> Is it enough just to use the "-water spce" flag in pdb2gmx to make sure >> I am using SPC/E water, while genbox uses the default spc216.gro? >> >> >> Regards, >> -- >> Suman Cha

[gmx-users] Gromacs-4.0.2: Compilation problem on IBM P690 Regatta System

usr/include/unistd.h", line 919.25: 1506-377 (I) The type "long long" of parameter 3 differs from the previous type "long". make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The er

[gmx-users] Re: Gromacs-4.0.2: Compilation problem on IBM P690 Regatta System

(int) See `config.log' for more details. Can anybody suggest what should I look for in the config.log file and how to go about solving it? Thanks. Regards, Suman Chakrabarty. On Tue, Nov 18, 2008 at 12:38 AM, Suman Chakrabarty <[EMAIL PROTECTED]> wrote: > Dear all, > >

Re: [gmx-users] Re: Gromacs-4.0.2: Compilation problem on IBM P690 Regatta System

On Tue, Nov 18, 2008 at 5:48 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > Suman Chakrabarty wrote: >> >> But now I have problem with the parallel (MPI) version. When I issue >> the command: >> ./configure --prefix=/home/hpcscratch/csdsuman/Gromacs

Re: [gmx-users] operating system

On Tue, Nov 18, 2008 at 7:59 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > > If you know its name, GROMACS is 99% likely to run on it. > > Mark Should be, but one must know the compilers and appropriate flags for compilation on obscure systems. I am having real tough time compiling Gromacs on an

Re: [gmx-users] GRACE installation

On Tue, Nov 18, 2008 at 9:19 AM, Q. Y. HUAN <[EMAIL PROTECTED]> wrote: > Dear gmx users and developers, > > Currently I am installing Grace into my computer, but the problem is that I > found difficulty to install it because there is no complete version of > installation file of it. After i insta

Re: [gmx-users] Re: Gromacs-4.0.2: Compilation problem on IBM P690 Regatta System

On Wed, Nov 19, 2008 at 5:57 AM, Mark Abraham <[EMAIL PROTECTED]> wrote: > Suman Chakrabarty wrote: > >> Now when I try to follow his script posted at >> http://www.gromacs.org/pipermail/gmx-users/2008-November/037973.html , >> I find that it does not work for me

Re: [gmx-users] Re: how to turn off the interamolecular interaction

On Wed, Nov 19, 2008 at 5:49 AM, Mark Abraham <[EMAIL PROTECTED]> wrote: > xianghong qi wrote: >> >> Dear all: >> >> I have a simple system which has two methane molecules with water. Now I >> need turn off the intermolecular interactions between these two methanes and >> just run >> simulation. S

[gmx-users] Incorrect download link in the Gromacs homepage

Hi, just wanted to point out that the link to the source package in Gromacs homepage reads as: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.0.2.tar.gz But it points to: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.0.tar.gz Regards, Suman. -- This message has been scanned for viruses and dan

[gmx-users] Gromacs-4.0.2: energy minimization error in parallel version

Dear all, I am trying to use mdrun_mpi for energy minimization over 2/4/8 nodes. But in every case the run gets aborted with the following error: --- Program mdrun_mpi, VERSION 4.0.2 Source code file: minimize.c, line: 404 Software inconsistenc

Re: [gmx-users] Gromacs-4.0.2: energy minimization error in parallel version

Hi Berk, Thanks for the update. I think steepest descent will be enough for me indeed. But I was not really sure about the preferred value for emtol ... I was using 1.0 following a colleague! Thanks again. Regards, Suman. On Sat, Nov 22, 2008 at 1:58 AM, Berk Hess <[EMAIL PROTECTED]> wrote: >

Re: [gmx-users] crash in gromacs-4.0.2 using vsites and 2fs t.s.

On Mon, Nov 24, 2008 at 11:46 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: >> Tcoupl = v-rescale >> tc_grps = system >> tau_t= 0.1 >> ref_t= 300.00 > > Maybe you want "Protein Non-Protein" instead of "system" here? But t

Re: [gmx-users] crash in gromacs-4.0.2 using vsites and 2fs t.s.

On Tue, Nov 25, 2008 at 1:40 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > Suman Chakrabarty wrote: >> >> On Mon, Nov 24, 2008 at 11:46 PM, Justin A. Lemkul <[EMAIL PROTECTED]> >> wrote: >>>> >>>> Tcoupl

[gmx-users] Analyzing a trajectory split over multiple files

Dear all, I have a very long trajectory split over a large number of files. What would be the most efficient way to use the analysis programs over them? Do they support multiple input for trajectory? Or I need to combine all files into a single one anyway? Please help. Regards, Suman. -- Thi

[gmx-users] Extracting the water molecules in hydration layer

Dear all, is there an easy way to extract only the water molecules in the hydration layer/shell around the protein/polymer chain? I need them both for visualization of the trajectory and some analysis. I can do this by writing my own program alright, but I wanted to know if there is any in-built

Re: [gmx-users] trr format file

On Thu, Nov 27, 2008 at 8:49 PM, Luca De Gaetani <[EMAIL PROTECTED]> wrote: > Dear GMX users, > > I want to use an external program to analyze gromacs .trr trajectory files. > I use FORTRAN. Can you indicate what is the FORMAT file of a .TRR file? That might be difficult. If the trajectory is no

Re: [gmx-users] Analyzing a trajectory split over multiple files

On Wed, Nov 26, 2008 at 2:19 PM, Omer Markovitch <[EMAIL PROTECTED]> wrote: > On Tue, Nov 25, 2008 at 01:47, Suman Chakrabarty <[EMAIL PROTECTED]> > wrote: >> >> Dear all, >> >> I have a very long trajectory split over a large number of files. What >

Re: [gmx-users] Analyzing a trajectory split over multiple files

On Fri, Nov 28, 2008 at 4:24 AM, Nicolas <[EMAIL PROTECTED]> wrote: > Suman Chakrabarty a écrit : >> It would have been much easier if there was some way to concatenate >> the multiple .xvg files easily. Also, the analysis programs should be >> able to export the ou

[gmx-users] Opinion requested regarding NVIDIA® Tesla™ Personal Supercomputer

ster built out of individual Intel Quad Core processors connected through Gigabit switch? If any of you have any experience and opinion regarding such systems, please share with me. It will be immensely helpful for us to make the decision. Thanks and regards, Suman C

[gmx-users] Question regarding trjorder

m asking a very naive question, but I could not find a general guideline to write the index file in the manual. Thanks and regards, Suman Chakrabarty. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-user

Re: [gmx-users] Question regarding trjorder

On Mon, 5 Jan 2009, Justin A. Lemkul wrote: [ Hydration Shell ] 1 2 3 n That will work to give you the hydration shell. Actually it seems I'll have to give the atom numbers instead of molecule numbers. When I used the above index group for testing, it just produced first n atoms of

Re: [gmx-users] force evaluation

lled > with zeros ? What about using the energygrp_excl parameter in the mdp file? It will turn off ALL non-bonded interactions though. Regards, Suman Chakrabarty. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/lis

[gmx-users] Problem with DMSO as solvent

er version. Regards, Suman Chakrabarty. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-us

Re: [gmx-users] Problem with DMSO as solvent

itp and dmso.gro accordingly and see what happens. A newbie question: what is the right way to search for existing DMSO parameters under any given force field, e.g. Gromos96 53a6 as you mentioned? Thanks and regards, Suman Chakrabarty. ___ gmx-users

Re: [gmx-users] Problem with DMSO as solvent

On Thu, Jan 8, 2009 at 4:42 AM, Justin A. Lemkul wrote: > > > Suman Chakrabarty wrote: >> >> On Thu, Jan 8, 2009 at 2:48 AM, Justin A. Lemkul wrote: >>>> >>>> 2. grompp with the modif

[gmx-users] Strange grompp error: System has non-zero total charge

= 1.2 fourier_spacing = 0.20 pme_order = 6 ewald_rtol = 1e-6 optimize_fft= yes constraints = none Thanks and regards, Suman Chakrabarty. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx

[gmx-users] pbc interference with g_dist

Hi, after spending a long time with a seemingly wrong result with g_dist, I discovered that g_dist actually uses pbc and nearest image convention to calculate the distance. As a result, the end-to-end distance of my polymer chain is calculated as 1.5 nm, while actually it should be 12.44 nm (box

Re: [gmx-users] Calculate asphericity of a group of atoms

ng_lists/users.php > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- === Suman Chakrabarty SSCU (Room # 106A) Indian Institute of Science, Bangalore, India. PIN: 560012 Mobile: +91 98

[gmx-users] Shake block crossing node boundaries

Hi, I am trying brownian dynamics simulation of a single polymer chain consisting of 100 atoms in vacuum. All bonds are constrained by LINCS. I am trying to use the particle decomposition scheme for parallel run since for a molecule in vacuum domain decomposition seems to be a waste. I am using th

[gmx-users] Questions about brownian/langevin dynamics of bead-spring polymers

simple brownian dynamics of an aliphatic chain? How is the information of water incorporated except for the random force and friction term? Which quantity makes the polymer hydrophobic/hydrophilic here? I would highly appreciate any help in these aspects. Best regards, Su

[gmx-users] How to display simulation box in VMD?

How do I display the actual simulation box in VMD for a gromacs configuration/trajectory? Is it possible? By default it shows only the axes. Regards, Suman Chakrabarty. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman

Re: [gmx-users] M*tif installation

at helps. Regards, Suman Chakrabarty. ___ 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)subscr

[gmx-users] Dissipative Particle Dynamics (DPD)

dynamic (Navier-Stokes) behaviour at large length and time scales, while DPD takes care of all these problems. In that case, wouldn't it be more appropriate to use this technique as a replacement of Brownian/Langevin dynamics? Regards, Suman Chakrabarty. ___

Re: [gmx-users] Dissipative Particle Dynamics (DPD)

Yang Ye wrote: > there is dpdmacs available.. Yes, I know. But that seems to support only harmonic potential for even non-bonded interaction (DPD manual page 4-5), which is rather unphysical and not suitable for my purpose. Regards, Suman Chakraba

Re: [gmx-users] Dissipative Particle Dynamics (DPD)

o the > main version. Each of the developers has its own research projects and > it hardly ever works just asking something you need to be implemented, > without providing the implementation. > > Maybe a bit disappointing, sorry. > > Cheers, > > Tsjerk > > On Tu