Re: [gmx-users] how to write .top file for a rigid molecule

Dear Jinyao, If you are talking about making the ring rigid and side group rigid, I would suggest adding a bunch of improper dihedrals to keep the molecule rigid. I found without adding the improper dihedrals that molecules that I would expect to be rigid were uncharacteristically

[gmx-users] .top file

hello everyone, while doing grompp for prest by giving command grompp -f *_md_water_prest.mdp -c *_md_water_em.gro -p *.top -o *_md_water_prest.tpr *i get the error* -- Program grompp, VERSION 4.0 Source code file: toppush.c, line: 1196 Fatal

[gmx-users] position restrain

Dear justin can I use pcouple=yes in pr.mdp ?what is defferent in my data when I use pcouple=no? best sh-karbalaee ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive

Re: [gmx-users] Gromacs 4 Scaling Benchmarks...

Am Mittwoch 12 November 2008 06:18:14 schrieb vivek sharma: Everybody thanks for your usefull suggestions.. What do you mean by % imbalance reported in log file. I don't know how to assign the specific load to PME, but I can see that around 37% of the computation is being used by PME. I am

Re: [gmx-users] density of the bilayer

On 12 Nov 2008 11:13:51 - minnale [EMAIL PROTECTED] wrote: Hi users, Intially I have run the simulation of the bilayer for 5ns then extended this to 20ns. When analyse density of the bilayer by considering trajectories of these different timings one at 5ns.xtc anonther at 20ns.xtc its

Re: [gmx-users] compilation of gmx-4.0.2

Thanks Mark and Justin, I got the script of installation of gromacs3.3.1 from the system manager. It works so far ... I attached it at the end (note: it is for double precision), it might help others. The mpicc was not found as mpcc was used instead. Best, XAvier

Re: [gmx-users] density of the bilayer

On 12 Nov 2008 11:41:54 - minnale [EMAIL PROTECTED] wrote: Thanks for your reply, In case of water density, starting of the water density will be for some time should come straight line in the graph later gradually reducing and goes to zero towards centre of the bilayer again it

RE: [gmx-users] GROMACS on Bluegene

Has there been any further discussion about fixing the issues discussed below regarding Blue Gene? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Thursday, October 16, 2008 10:43 PM To: Gromacs Users Subject: [gmx-users] GROMACS on

[gmx-users] small protein big frozen group - exploding

Dear, I am simulating a small protein (less then 50 amino acids) at room temperature, with no additional atoms and/or molecules and/or ions. The simulations seems to proceed ok (in terms of avg. kinetic energy and other energy terms). Then, I take the same protein, and introduce a surface to the

[gmx-users] Force Fields for Solids

Hi, I read that some have been using GROMACS to model epoxy polymers, and I'm wondering which force field you've been using. I'd ideally like to implement the new DFTB+ code into GROMACS to run some QM/MM simulations of epoxy/TiO2 nanocomposites. Thanks, Chris Rowan

Re: Re: [gmx-users] density of the bilayer

Thanks for your reply, In case of water density, starting of the water density will be for some time should come straight line in the graph later gradually reducing and goes to zero towards centre of the bilayer again it increases and stop going the water density. but in my case starting

[gmx-users] problem installing FFTW

  Hi everybody, I am trying to install FFTW and gromacs 3.3.2 into my Mac 10.4.1. I got the source code fftw-3.0.1.tar.gz. from GROMACS homepage . However, when I tried to configure FFTW, I found the message dummy main to link with Fortran 77 libraries... unknown configure:

Re: [gmx-users] problem installing FFTW

sarbani chattopadhyay wrote: Hi everybody, I am trying to install FFTW and gromacs 3.3.2 into my Mac 10.4.1. I got the source code fftw-3.0.1.tar.gz. from GROMACS homepage . However, when I tried to configure FFTW, I found the message dummy main to link with Fortran 77

[gmx-users] problem with pulling (afm_rate is not equal to real pull-velocity)

Dear all, i have with Gromacs 3.3.3 problem with the afm-pulling (the velocity are not correct) My system consists of ureas with short alkane linkers (see picture below) +___+___+ ||| x x x x x x ||| * x are the ureas (which form

[gmx-users] trjconv write frames to separate files

Hi, i'm trying to write each frame from the bebining time=0.0 to the end time=6000 to a separate file, but it writes only the 1frame at time 0.0: trjconv -f 1ktz_p1_em.gro -s 1ktz_p1_em.tpr -o 1ktz_0.pdb -b 0.0 -e 6000.0 -sep Reading frames from gro file 'GROningen MAchine for Chemical

Re: [gmx-users] trjconv write frames to separate files

tatsiana kirys wrote: Hi, i'm trying to write each frame from the bebining time=0.0 to the end time=6000 to a separate file, but it writes only the 1frame at time 0.0: trjconv -f 1ktz_p1_em.gro -s 1ktz_p1_em.tpr -o 1ktz_0.pdb -b 0.0 -e 6000.0 -sep Reading frames from gro file 'GROningen

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 fixing the

Re: [gmx-users] position restrain

shahrbanoo karbalaee wrote: Dear justin can I use pcouple=yes in pr.mdp ?what is defferent in my data when I use pcouple=no? pcoupl = yes doesn't do anything. You have to specify the type of pressure coupling (grompp should tell you that). For a discussion of the differences of

[gmx-users] density of the bilayer

Hi users, Intially I have run the simulation of the bilayer for 5ns then extended this to 20ns. When analyse density of the bilayer by considering trajectories of these different timings one at 5ns.xtc anonther at 20ns.xtc its showing almost same density values how come it is possible? the

[gmx-users] Re:density of the bilayer

Thanks alot for your reply In case of water density, starting of the water density will be for some time should come straight line in the graph later gradually reducing and goes to zero towards centre of the bilayer again it increases and stop going the water density. but in my case

Re: [gmx-users] Warning in compiling GMX4.0.2

On Wed, 12 Nov 2008 11:48:11 +0100 Xavier Periole [EMAIL PROTECTED] wrote: Here a following up of the compilation on the IBM. I got the following warning: 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to

[gmx-users] Re: grompp NOTE mdp file concerning steps

Hello, searching further the issue, I realized that no more than 32299167 number of steps can be used. In case someone uses more, the note I describe makes its appearance. Is this a new limit? Regards, Nikos --- Claus Valka [EMAIL PROTECTED] schrieb am Mi, 12.11.2008: Von: Claus Valka [EMAIL

[gmx-users] Versions of analysis programs

Hi, I've noticed that the VERSION entry of the analysis programs in GMX 4.0.2 is 3.2.0 or 3.3.2, whereas in GMX 3.3.3 it's 3.3.3. Is that just a typo? Thanks, Ran. ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Warning in compiling GMX4.0.2

Mark Abraham wrote: Xavier Periole wrote: Here a following up of the compilation on the IBM. I got the following warning: 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT

Re: [gmx-users] Warning in compiling GMX4.0.2

Xavier Periole wrote: Here a following up of the compilation on the IBM. I got the following warning: 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more

[gmx-users] Is it normal for mdrun to go very slow when a large number of 'energygrps' user-defined potentials are used? (This re-post is easier to read)

Dear GROMACS users, I am hoping to get some information from you experts regarding the use of user-defined potentials (table*.xvg). With the help of the GROMACS manual and several posts in the mailing list, I have been able to make user-defined potential functions that I would like to apply to

Re: [gmx-users] GROMACS on Bluegene

Mathias has updated the wiki: http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene On Wed, Nov 12, 2008 at 11:57 AM, Suman Chakrabarty [EMAIL PROTECTED] wrote: 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

[gmx-users] centre of the system: error

Hi all, I am trying to make centre of the bilayer so I used following command line trjconv -f 20nspopc.xtc -centre rect -o 20nstrjout.xtc -n water.ndx based on http://www.gromacs.org/pipermail/gmx-users/2003-June/005995.html here I selected 3 (solution) again 3 (solution) for output of the

[gmx-users] Is it normal for mdrun to go very slow when a large number of 'energygrps' user-defined potentials are used?

Dear GROMACS users, I am hoping to get some information from you experts regarding the use of user-defined potentials (table*.xvg). With the help of the GROMACS manual and several posts in the mailing list, I have been able to make user-defined potential functions that I would like to apply

Re: [gmx-users] Re: grompp NOTE mdp file concerning steps

Hi Nikos, You mention it raises a note. What happens to the .tpr file? Can you look for nsteps in the output from gmxdump? Cheers, Tsjerk On Wed, Nov 12, 2008 at 2:45 PM, Claus Valka [EMAIL PROTECTED] wrote: Hello, searching further the issue, I realized that no more than 32299167 number of

Re: [gmx-users] .top file

Bhawana Gupta wrote: hello everyone, while doing grompp for prest by giving command grompp -f *_md_water_prest.mdp -c *_md_water_em.gro -p *.top -o *_md_water_prest.tpr *i get the error* -- Program grompp, VERSION 4.0 Source code file:

[gmx-users] grompp NOTE mdp file concerning steps

Hello, I'm using gromacs version 4.0 and when I type : grompp -f file.mdp -c file.gro -p topol.top I get this note: NOTE 1 [file file.mdp, line unknown]: and nothing else. I checked my mdp file and I noticed than when I give 5000 steps I get this error (steps with more than 7 digits). If

Re: [gmx-users] GROMACS on Bluegene

Roland Schulz wrote: Mathias has updated the wiki: http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene That's great, there's a lot of useful info here. There are still outstanding issues with the kernels - see the discussion here and my various bugzillas

Re: [gmx-users] Is it normal for mdrun to go very slow when a large number of 'energygrps' user-defined potentials are used?

Musselman, Eli D wrote: This works great but ***here’s the problem*** : *the simulations run exceedingly slow when I use such a high number of defined ‘energygrps’*. Without using the user defined potential functions I was getting roughly 25 ns/day (which, as always with GROMACS, is amazingly

[gmx-users] Warning in compiling GMX4.0.2

Here a following up of the compilation on the IBM. I got the following warning: 1500-036: (I) The NOSTRICT option (default at OPT(3)) has the potential to alter the semantics of a program. Please refer to documentation on the STRICT/NOSTRICT option for more information. Should that be a

Re: [gmx-users] GROMACS on Bluegene

Mike Hanby wrote: I keep failing the ../configure when I have -lmass or -lmassv in LIBS for the frontend gromacs configure: - checking for C compiler default output file name... configure: error: C compiler cannot create executables

[gmx-users] charge distribution

Hi, gmx-usrs, I want to ask for a problem on the charge distribution. I simulate the sodium dodecylbenzenesulfonate and its homologues in solution using the gromos96 force field. I can not find the similar atom type as replace in the gromos96 force field . How do I define every atomic charge?

Re: [gmx-users] charge distribution

Hongyan Xiao wrote: Hi, gmx-usrs, I want to ask for a problem on the charge distribution. I simulate the sodium dodecylbenzenesulfonate and its homologues in solution using the gromos96 force field. I can not find the similar atom type as replace in the gromos96 force field . How do I

[gmx-users] charge distribution

Dear Justin, For sodium dodecylbenzenesulfonate(C12H25C6H4SO3Na), the charges of S and O in S03- , I cannot find the suitable charge. Forthermore, the carbon in benzene connecting the SO3- is setted to be zero, I think that there may be questionable. The polarization of SO3- is very large.

[gmx-users] problem with FFTW installation

 Hi everybody, I am trying to install FFTW and gromacs 3.3.2 into my Mac 10.4.1. I got the source code fftw-3.0.1.tar.gz. from GROMACS homepage . However, when I tried to configure FFTW, I found the message dummy main to link with Fortran 77 libraries... unknown configure:

Re: [gmx-users] problem with FFTW installation

sarbani chattopadhyay wrote: Hi everybody, I am trying to install FFTW and gromacs 3.3.2 into my Mac 10.4.1. I got the source code fftw-3.0.1.tar.gz. from GROMACS homepage . However, when I tried to configure FFTW, I found the message dummy main to link with Fortran 77

Re: Re: [gmx-users] problem with FFTW installation

 Thank you Mark. I will continue with the installation. Sarbani On Thu, 13 Nov 2008 Mark Abraham wrote : sarbani chattopadhyay wrote: Hi everybody, I am trying to install FFTW and gromacs 3.3.2 into my Mac 10.4.1. I got the source code fftw-3.0.1.tar.gz. from GROMACS

[gmx-users] can't find fftw3f library

  Hi everybody, I am trying to install gromacs3.3.2 into my Mac Os X 10.4.1 using the source code. I have installed FFTW and the library files of fftw are in /usr/local/lib. However when I try to configure gromacs, it's gives an error : Cannot find fftw3f library. Going

Re: [gmx-users] can't find fftw3f library

sarbani chattopadhyay wrote: Hi everybody, I am trying to install gromacs3.3.2 into my Mac Os X 10.4.1 using the source code. I have installed FFTW and the library files of fftw are in /usr/local/lib. However when I try to configure gromacs, it's gives an error : Cannot