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

vivek sharma wrote: 2008/11/11 Justin A. Lemkul <[EMAIL PROTECTED] > vivek sharma wrote: HI MArtin, I am using here the infiniband having speed more than 10 gbps..Can you suggest some option to scale better in this case. What % imb

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

2008/11/11 Justin A. Lemkul <[EMAIL PROTECTED]> > > > vivek sharma wrote: > >> HI MArtin, >> I am using here the infiniband having speed more than 10 gbps..Can you >> suggest some option to scale better in this case. >> >> > What % imbalance is being reported in the log file? What fraction of the

Re: [gmx-users] distance restrain

Pathumwadee Intharathep wrote: Dear gmx-users, How can I make the distance restrain between molecules such as protein and ligand? By introducing them in your .top file. Check out the relevant sections of chapters 4 and 5 of the manual. Mark ___

[gmx-users] distance restrain

Dear gmx-users,   How can I make the distance restrain between molecules such as protein and ligand?   thanks in advance   pathum   ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please searc

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

Jinyao Wang wrote: > gmx-users, > I am goning to carry out a rigid system system simulation for Benzaldehyde. > Atom charges,Bonds and Angles come from Gaussion03 computation. LJ > interaction parameters come from oplsaa forcefield. I don't know how to deal > with rigid molecules in gromacs. So

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

Jinyao Wang wrote: gmx-users, I am goning to carry out a rigid system system simulation for Benzaldehyde. Atom charges,Bonds and Angles come from Gaussion03 computation. LJ interaction parameters come from oplsaa forcefield. I don't know how to deal with rigid molecules in gromacs. So I cou

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

gmx-users, I am goning to carry out a rigid system system simulation for Benzaldehyde. Atom charges,Bonds and Angles come from Gaussion03 computation. LJ interaction parameters come from oplsaa forcefield. I don't know how to deal with rigid molecules in gromacs. So I couldnot know how to write

[gmx-users] appropriate time constant and forces for distance restraints

Hi, all, Question #1: Appropriate time constant for distance restraints. I am docking a small molecule to a macromolecule and I was wondering what would be an appropriate value for a time constant. I was thinking that a time constant that is equal to the time for a single rotation woul

Re: [gmx-users] Library file ffG43a1.n2t not found

ROHIT MALSHE wrote: Hi all, I was trying to use x2top to generate a topology file, but I got following error when I selected a forcefield type. Library file ffG43a1.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) Pl

Re: [gmx-users] Library file ffG43a1.n2t not found

ROHIT MALSHE wrote: Hi all, I was trying to use x2top to generate a topology file, but I got following error when I selected a forcefield type. Library file ffG43a1.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable)

Re: [gmx-users] question on diffusion during MD

Ramon Crehuet wrote: Dear gmx users, I am running MD simulations of a tetrameric protein and as I want to compare with neutron scattering data I need to take into account protein diffusion implicitly. If I use /nstcomm = 1/ (default value) the simulation (1 ns) leads to a minimal random motion (

Re: [gmx-users] xdrf Fortran program and g_traj

Shaghayegh Vafaei wrote: Hi all, I was wondering if somebody has worked or used the xdrf Fortran program in order to read the coordinates from a .xtc file. There are 6 errors after compiling the program . The subroutines are not included there and I couldn't find them in the links -> http://hpcv

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

Xavier Periole wrote: Dears, my turn to ask a stupid question: I am trying to install gmx402 on a IBM pSeries 575 CPUs: dual core IBM Power6 when running the command: ./configure --enable-mpi --prefix==/home/X/gmx402/ I run very into the error: . . checking size of int... config

Re: [gmx-users] position and distance restrain

Pathumwadee Intharathep wrote: Dear gmx-user, Do I define position and distance restrain simulteneusly? my md.mdp has set as below but it works only for position restrain. Right, because multiple instances of the same parameter get discarded. Combine both define statements on one line:

[gmx-users] Library file ffG43a1.n2t not found

Hi all, I was trying to use x2top to generate a topology file, but I got following error when I selected a forcefield type. Library file ffG43a1.n2t not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) Please let me know what

[gmx-users] position and distance restrain

Dear  gmx-user,   Do I define position and distance restrain simulteneusly? my md.mdp has set as below but it works only for position restrain.   title   = M2_amand in POPC cpp =  /lib/cpp define  =  -DPOSRES define  =  -DDISRES constraints  

[gmx-users] Inconsistent shifts

Hi I am a new Gromacs user.I am trying to study the adsorption of proteins on graphite surface.In mdp file I took the option pbc=full. When I am running a simulation for 5 ns, I am getting the output with out any warning. But when I am analysing the results using h_bond , g_gyrate and do_dssp, I a

Re: [gmx-users] system explodes

Thank you. I will do so. kind regards, Andrea 2008/11/11 Justin A. Lemkul <[EMAIL PROTECTED]>: > > > Andrea Muntean wrote: >> >> I am simulating one chain of PS. The box is produced by pdb2gmx. If I >> run simulations with timestep 0.1 fs up to 0.4 fs everything seem to >> be ok. With 1 fs (which

Re: [gmx-users] the temperature effect in the simulation

He, Yang wrote: Hi Justin, Yes, I am trying the course-grain model using gromacs, an absolute newer. My current model is not complex, just including 22 big atoms, only 4 base pair. What is the use of summing the entire base into one particle? The only coarse-grain FF I know anything about

Re: [gmx-users] system explodes

Andrea Muntean wrote: I am simulating one chain of PS. The box is produced by pdb2gmx. If I run simulations with timestep 0.1 fs up to 0.4 fs everything seem to be ok. With 1 fs (which should be a normal time for my system) I would get the following warning: Warning: 1-4 interaction between 29

[gmx-users] system explodes

I am simulating one chain of PS. The box is produced by pdb2gmx. If I run simulations with timestep 0.1 fs up to 0.4 fs everything seem to be ok. With 1 fs (which should be a normal time for my system) I would get the following warning: Warning: 1-4 interaction between 290 and 299 at distance 108.

Re: [gmx-users] the temperature effect in the simulation

He, Yang wrote: Hi Justin, In my case, my box size is adequate to avoid interaction of periodic images of your DNA .For this point, I think is ok. In fact, when I run this simulation especially for the low temperature, one atom's(Tb1) behavior is strange .No matter how low the temperature

Re: [gmx-users] the Temperature in the mdp.file

Hi He Yang, I've never worked with DNA simulations before, but I don't think you should have a timestep of 0.0001 ps. For proteins, people commonly use 0.002ps, i.e 20 x larger than what you are using. The number of steps you are using is quite small too. Also, where did you get your rlist =

RE: [gmx-users] the temperature effect in the simulation

Hi Yuguang, when I use the command ngmx to show the trajectory , I just choose the DNA group not including the water. Any suggestions ? Thank you very much. Yang From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mu Yuguang (Dr) [EMAIL PROTECTED] Se

Re: [gmx-users] the temperature effect in the simulation

He, Yang wrote: Hi Justin, My box size is 3.13690 3.73000 2.7 and I use the user-defined potential functions. Is that box size adequate to avoid interaction of periodic images of your DNA? Typical B-DNA is about 2 nm wide, if 2.7 nm is the width of your box, I'd bet you're gett

Re: [gmx-users] ionic liquid

Hi naimah. Sorry for the late replay, but I was travelling. What kind of ionic liquids are you interested in? If they are the dialkyl-immidazolium ones, I'm doing simulations on these systems for quite some time now (please look at these references: Journal of Physical Chemistry B, v. 112, p. 8966

RE: [gmx-users] the temperature effect in the simulation

Hi Justin, My box size is 3.13690 3.73000 2.7 and I use the user-defined potential functions. #define _FF_GROMACS #define _FF_GROMACS1 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 1.0 1.0

RE: [gmx-users] the temperature effect in the simulation

Do you have water ? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nicolas Sapay Sent: 2008年11月12日 4:15 To: Discussion list for GROMACS users Subject: Re: [gmx-users] the temperature effect in the simulation He, Yang wrote: > Hi all users, > > When I cha

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

On Tue, 11 Nov 2008 14:44:23 -0500 "Justin A. Lemkul" <[EMAIL PROTECTED]> wrote: Xavier Periole wrote: Dears, my turn to ask a stupid question: I am trying to install gmx402 on a IBM pSeries 575 CPUs: dual core IBM Power6 when running the command: ./configure --enable-mpi --prefix==/home/

Re: [gmx-users] the temperature effect in the simulation

He, Yang wrote: Hi all users, When I change the temperature to try to get different disassociation about the two DNA's strands. But even I change the value of temperature by 0K in the mdp file , ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen

Re: [gmx-users] the temperature effect in the simulation

He, Yang wrote: Hi all users, When I change the temperature to try to get different disassociation about the two DNA's strands. But even I change the value of temperature by 0K in the mdp file , ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berends

[gmx-users] the temperature effect in the simulation

Hi all users, When I change the temperature to try to get different disassociation about the two DNA's strands. But even I change the value of temperature by 0K in the mdp file , ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = berendsen ; Groups to coupl

RE: [gmx-users] the Temperature in the mdp.file

Hi Yang Ye, Thank you for your reply. When I change the temperature, the disassociation about the two strands of DNA always happened even though the temperature is reduced to 0K. It is absolutely impossible. I think it is a real disassociation. So I am confused about the phenomenon . Any furth

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

Xavier Periole wrote: Dears, my turn to ask a stupid question: I am trying to install gmx402 on a IBM pSeries 575 CPUs: dual core IBM Power6 when running the command: ./configure --enable-mpi --prefix==/home/X/gmx402/ I run very into the error: . . checking size of int... conf

[gmx-users] compilation of gmx-4.0.2

Dears, my turn to ask a stupid question: I am trying to install gmx402 on a IBM pSeries 575 CPUs: dual core IBM Power6 when running the command: ./configure --enable-mpi --prefix==/home/X/gmx402/ I run very into the error: . . checking size of int... configure: error: cannot comp

[gmx-users] xdrf Fortran program and g_traj

Hi all, I was wondering if somebody has worked or used the xdrf Fortran program in order to read the coordinates from a .xtc file. There are 6 errors after compiling the program . The subroutines are not included there and I couldn't find them in the links -> http://hpcv100.rc.rug.nl/xdrf.html ,

Re: [gmx-users] continuation options

On Nov 11, 2008, at 15:39 , Berk Hess wrote: > With Gromacs 4.0 I get this message: > > NOTE: The simulation uses pressure coupling and/or stochastic dynamics. > tpbconv can not provide binary identical continuation. > If you want that, supply a checkpoint file to mdrun > > Is it possible to

[gmx-users] question on diffusion during MD

Dear gmx users, I am running MD simulations of a tetrameric protein and as I want to compare with neutron scattering data I need to take into account protein diffusion implicitly. If I use /nstcomm = 1/ (default value) the simulation (1 ns) leads to a minimal random motion (traslational and rotati

Re: [gmx-users] flood of gmx's mails in my mailbox

...or use gmail. Tsjerk On Tue, Nov 11, 2008 at 1:31 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > Pathumwadee Intharathep wrote: >> >> Dear gmx-user, >> My mailbox has flood of gmx's mails. What should I do to digest them. >> > > Use the WWW interface to change your preferences to diges

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

A page on the wiki with further information and hints would be nice. Topic: "improving performance with GMX4" or "Pimp my GMX4" ;-) The beta manualpage of mdrun (version4) is not very comprehensible/user friendly in my eyes. - Christian On Tue, 2008-11-11 at 09:12 -0500, Justin A. Lemkul wrote:

RE: [gmx-users] continuation options

> From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Date: Tue, 11 Nov 2008 14:50:46 +0100 > Subject: [gmx-users] continuation options > > With Gromacs 4.0 I get this message: > > NOTE: The simulation uses pressure coupling and/or stochastic dynamics. > tpbconv can not provide binary identi

RE: [gmx-users] FFTW problem for Gromacs4

Also, I'm not positive, but I believe the switch should be "--enable-float" not "--enable-floats", so your fftw compile probably didn't build the float version. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jussi Lehtola Sent: Tuesday, November 11, 2008

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

vivek sharma wrote: HI MArtin, I am using here the infiniband having speed more than 10 gbps..Can you suggest some option to scale better in this case. What % imbalance is being reported in the log file? What fraction of the load is being assigned to PME, from grompp? How many processor

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

vivek sharma wrote: Hi All, one thing I forgot to mention I am getting here around 6 ns/day...for a protein of size around 2600 atoms.. Much more relevant is how much water... You can also be rate limited by I/O if you have poor hardware and/or are writing to disk excessively. Mark ___

[gmx-users] continuation options

With Gromacs 4.0 I get this message: NOTE: The simulation uses pressure coupling and/or stochastic dynamics. tpbconv can not provide binary identical continuation. If you want that, supply a checkpoint file to mdrun Is it possible to extend a trajectory with mdrun, a checkpoint file and a new

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

Hi All, one thing I forgot to mention I am getting here around 6 ns/day...for a protein of size around 2600 atoms.. With Thanks, Vivek 2008/11/11 vivek sharma <[EMAIL PROTECTED]> > HI MArtin, > I am using here the infiniband having speed more than 10 gbps..Can you > suggest some option to scale

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

HI MArtin, I am using here the infiniband having speed more than 10 gbps..Can you suggest some option to scale better in this case. With Thanks, Vivek 2008/11/11 Martin Höfling <[EMAIL PROTECTED]> > Am Dienstag 11 November 2008 12:06:06 schrieb vivek sharma: > > > > I have also tried scaling gro

Re: [gmx-users] flood of gmx's mails in my mailbox

Pathumwadee Intharathep wrote: Dear gmx-user, My mailbox has flood of gmx's mails. What should I do to digest them. Use the WWW interface to change your preferences to digest form. -Justin Best regards, pathumwadee

[gmx-users] flood of gmx's mails in my mailbox

Dear gmx-user,   My mailbox has flood of gmx's mails. What should I do to digest them.   Best regards,   pathumwadee  ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive a

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

Hi Vivek, if you use separate PME nodes (-npme) then one group of the processors will calculate the long-range (reciprocal space) part while the remaining processors do the short-range (direct space) part of the Coulomb forces. The goal is to choose the number of nodes in both groups such

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

Am Dienstag 11 November 2008 12:06:06 schrieb vivek sharma: > I have also tried scaling gromacs for a number of nodes but was not > able to optimize it beyond 20 processor..on 20 nodes i.e. 1 processor per As mentioned before, performance strongly depends on the type of interconnect you're

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

vivek sharma wrote: Hi Carsten, I have also tried scaling gromacs for a number of nodes but was not able to optimize it beyond 20 processor..on 20 nodes i.e. 1 processor per node.. I am not getting the point of optimizing PME for the number of nodes, is it like we can change the paramete

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

Hi Carsten, I have also tried scaling gromacs for a number of nodes but was not able to optimize it beyond 20 processor..on 20 nodes i.e. 1 processor per node.. I am not getting the point of optimizing PME for the number of nodes, is it like we can change the parameters for PME for MDS or using

Re: [gmx-users] questions in Running MDS over docked poses

vivek sharma wrote: hi Justin, Thanks for your reply... I am interested in looking for the stability of the docked pose, by applying some temperature variation in the molecule. If I am applying temperature variation then should I use pressure coupling simultaneously. Well that's going to de

Re: [gmx-users] FFTW problem for Gromacs4

On Tue, 2008-11-11 at 14:32 +0530, Anirban Ghosh wrote: > > Hi ALL, > > I am trying to install Gromacs4 on Fedora9. I have installed fftw3.1.3 > with the following option: If you don't want to use any special compiler to compile GROMACS just use the version included in the distribution:

Re: [gmx-users] FFTW problem for Gromacs4

On Tue, 11 Nov 2008 14:32:32 +0530 (IST) Anirban Ghosh <[EMAIL PROTECTED]> wrote: Hi ALL, I am trying to install Gromacs4 on Fedora9. I have installed fftw3.1.3 with the following option: ./configure --enable-floats --enable-threads --prefix=/home/anirban/Software/fftw-3.1.3 no "s" at "-

[gmx-users] FFTW problem for Gromacs4

Hi ALL, I am trying to install Gromacs4 on Fedora9. I have installed fftw3.1.3 with the following option: ./configure --enable-floats --enable-threads --prefix=/home/anirban/Software/fftw-3.1.3 Then I used the following commands to make links: export CPPFLAGS=-I/home/anirban/Software/fftw-