Re: [gmx-users] dihedral constrain

lmao wrote: Hi, I want to put dihedral constrain on the transmembrane helices of my protein using phi and psi angles to keep it helical during MD run. I wonder how I can do this in Gromacs becasue I could not find it from the manual. I am using Gromacs-3.2.1. Thanks. Section 4.3.3 in the c

[gmx-users] dihedral constrain

Hi, I want to put dihedral constrain on the transmembrane helices of my protein using phi and psi angles to keep it helical during MD run. I wonder how I can do this in Gromacs becasue I could not find it from the manual. I am using Gromacs-3.2.1. Thanks. lmao __

RE: [gmx-users] compiling gromacs with cygwin

Hi Vanessa, how about the following faqs. http://www.gromacs.org/faq/index.php#fftw http://www.gromacs.org/faq/index.php#fftwlocation Regards, MAKOTO > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Vanessa Oklejas > Sent: Friday, April 14, 2006 8:

Re: [gmx-users] compiling gromacs with cygwin

I'm pretty sure that GROMACS prior to version 3.3 requires FFTW version 2 and won't work with FFTW 3. 3.3 and later are compatible with either version. David On 4/13/06, Vanessa Oklejas <[EMAIL PROTECTED]> wrote: > Hi All, > > I want to get gromacs v 3.1.0 running on my PC via cygwin. I have >

[gmx-users] compiling gromacs with cygwin

Hi All, I want to get gromacs v 3.1.0 running on my PC via cygwin. I have been able to compile fftw-3.0.1 but, when I try to execute the configure file, it terminates when it tries (unsuccessfully) to find the fftw library. Anyone have experience with this? Thanks, Vanessa ___

[gmx-users] Re: Using Pull code with Coarse grain model

Hi Dr .Warren, Yes I tried without pull code. Atleast I ran for 10ns and it works (i.e DPPC bilayer with a butane molecule in the water). I am not sure why it doesnt work with pull code. Mohan On 13/04/06, [EMAIL PROTECTED] <[EMAIL PROTECTED] > wrote:Send gmx-users mailing list submissions to  

Re: [gmx-users] Radial distance restraints

Bob Johnson wrote: Hello everyone, Is there any way to use radial distance restraints? For example, my system is cylindrically symmetric (it's a carbon nanotube) and I would like to restrain molecules to a certain distance away from the nanotube axis. Obviously, I don't care if they the slide alo

[gmx-users] Radial distance restraints

Hello everyone, Is there any way to use radial distance restraints? For example, my system is cylindrically symmetric (it's a carbon nanotube) and I would like to restrain molecules to a certain distance away from the nanotube axis. Obviously, I don't care if they the slide along the z-axis or chan

[gmx-users] re: Does mdrun know when other gromacs programs move its destination .xtc?

Fantastic! Just another reason to love and prefer Gromacs. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [

Re: [gmx-users] Does mdrun know when other gromacs programs move its destination .xtc?

[EMAIL PROTECTED] wrote: When an output .xtc destination of mdrun is backed up while the original version of mdrun is still running, does mdrun know and does the output get handled correctly? No, but it works the way you'd want it to. So two versions of mdrun are running simultaneously in the

Re: [gmx-users] REMD

Dear David, I believe it runs in two processors because I can get two log files. I tried to use mpirun, the computer complains that command mpirun (or mpi_run) not found. Replica1.log stops at: Rel. Constraint Deviation: Maxbetween atoms RMS Then I search where those messages are from i

[gmx-users] Does mdrun know when other gromacs programs move its destination .xtc?

When an output .xtc destination of mdrun is backed up while the original version of mdrun is still running, does mdrun know and does the output get handled correctly? here is what happened to me: 1) mdrun produces traj.xtc 2) Beleiving that mdrun had died due to a hardware error, I restarted the

[gmx-users] Re: covariance matrix

Hi Tsjerk, You are absolutely right! :-) Thanks for your help!  Regards, Maki Yoshisawa Celebrate Yahoo! JAPAN 10th Anniversary ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)

Re: [gmx-users] REMD

Dongsheng Zhang wrote: Dear David, I forgot one more information. The computer administrator told me I did not need to use mpirun. As I told you in the previous email, I have done tests for parallel computing. It worked fine. try it with mpirun anyway. I suspect you are just running a single

Re: [gmx-users] covariance matrix

Hi Maki,Personally, for the fifth row I would expecty1x2 y1y2 y1z2etc.. Inferred from the logic of the first four rows. But that's the best I can do without having a look at the code ;)Cheers, TsjerkOn 4/13/06, [EMAIL PROTECTED] <[EMAIL PROTECTED] > wrote: Hi! I am not quite sure I have understood

[gmx-users] covariance matrix

Hi! I am not quite sure I have understood the way the ASCII version of the covariance matrix (-ASCII option of g_covar) has been constructed... In my test system I have 3 atoms - this will give a 9X9 cov. matrix. In the help of g_covar the order the covar.dat file is: first row: x1x1 x1y1 x1z1  se

Re: [gmx-users] REMD

Dear David, I forgot one more information. The computer administrator told me I did not need to use mpirun. As I told you in the previous email, I have done tests for parallel computing. It worked fine. Dongsheng On Thu, 2006-04-13 at 09:52 +0200, David van der Spoel wrote: > Dongsheng Zhang wro

Re: [gmx-users] REMD

Dear David, The commands I used are as following: grompp -f replica0.mdp -c confout.gro -p topol.top -o replica0 to get replica0.tpr grompp -f replica1.mdp -c confout.gro -p topol.top -o replica1 to get replica1.tpr the script I used is: #PBS -S /bin/ksh -q sp_large ### CPU number #PBS -l node

Re: [gmx-users] MSD

Well. I think I agree with David 100 cations and 100 anions without solvent (am I correct?)... probably your system is freezing and an evidence of this is that the slope of your MSD graph tends to zero, so your D tends to zero too. But considering what you said about ACFs and RDFs, I thi

Re: [gmx-users] seperating bilayers (again)

15, 20, even 30 nm all result in the same effect, just at different rates. I didn't try anything larger than that - several of my systems would be dangerously close to being under 2x the cutoff radius across if I went even slightly higher. --- Eric Jakobsson <[EMAIL PROTECTED]> wrote: > What is

Re: [gmx-users] MSD

Roman Holomb wrote: Dear colleagues, Thanks for reply! Maybe I'm doing something wrong with using g_msd . no your system is freezing. I have computed MD (5ns) for system containing 100 anion and 100 cation molecules. Results of ACFs, RDFs look good but not MSD So I have 2_emi_BF4

[gmx-users] MSD

Dear colleagues, Thanks for reply! Maybe I'm doing something wrong with using g_msd . I have computed MD (5ns) for system containing 100 anion and 100 cation molecules. Results of ACFs, RDFs look good but not MSD So I have 2_emi_BF4_100.tpr, 2_emi_BF4_100.trr, 2_indexEMI.ndx files.

[gmx-users] Re: Can you help me?

Dr. Dong XY wrote: Hello, K. Anton Feenstra I'm a student of Tianjin University of China. I want to get the chemical unfolding structure of protein.But I can't minimize the mixture. I always get the following cues: ~~~ Stepsize too

Re: [gmx-users] Using Pull code with Coarse grain model

Mohan Boggara wrote: Hi all, I am trying to use the pull code for constrained force method in a coarse grain dppc bilayer model developed by Dr. S.J. Marrink. But I am getting error message Warning: pressure scaling > 1% . The problem persist even after I changed the tau_p from 1.0 to 1.5. H

Re: [gmx-users] REMD

Dongsheng Zhang wrote: dear Mark, Thank you very much for your prompt reply. I try to use parallel computing. It works fine. for example: grompp -f -c -p -o replica0 -np 2 -sort -shuffle to get replica0.tpr then, mdrun_mpi -np 2 -s replica0.tpr please give EX