Re: [gmx-users] openmpi
Hi, I'm using openmpi on our 24-nodes 2 cores each cluster without any problem so far. I run my jobs under torque and I did not change any of default settings. With my system it scales rather well on 4 nodes, but I have no problems with running more. Grzegorz Wieczorek Department of Bioinformatics Institute of Biochemistry and Biophysics Polish Academy of Sciences ul. Pawinskiego 5a 02-106 Warszawa, Poland On Thu, 14 Sep 2006, [EMAIL PROTECTED] wrote: Anyone using openmpi for parallel gromacs? If so, how to set the maximum short tcp length? I have tried some things unsuccessfully which are posted at the open mpi site: http://www.open-mpi.org/community/lists/users/2006/09/1864.php ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bond lost!
zzhwise1 wrote: good everyone i have 2 questions : 1) when i optimized my system of CH3(CH2)13COOH chains with l-bfgs for 5000steps,but it stopped at 467th step,and i found the conformation break,8chains'lost the C-OH bonds,why there was this and what cause this?was this the wrong itp or mdp? Your topology was not correct. Compare the contents of the .top file with the .itp file it was sourced from. 2) when i change the mdp with md,then show the gro atomnumber not incorred with top?why?i still could not find out the reason! I can't understand this. You need to describe the problem fully, include contents of small files where appropriate, and quote the feedback you get from the gromacs tools. Or you could employ a mind-reader. I know what's cheaper :-) Mark ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] The molecule size
Hi: Two meltmodels were built for polyethylene (PE) and polyvinylmethylether (PVME) melt with PBC condition. The density of both melt model agree with experimenal value well.But when one check the radius of gyration (Rg) of them, both of them were too small to accept as follows. The Rg for PE (C1000) is just 28 angstrom. It means the infinite charaterastic ratio (Cinf) for the polymer is just about 2 which is much smaller than scatter experimental value about 7. The Rg for PVME (C44) melt is about 6.6 angstrom. It means the Cinf for the polymer is just 2.5 which is much smaller than scatter experimental value 8-10. Can these results be accepted? Is there any fault in force field? gromos96a Thanks in advance. *Ji QingInstitute of Chemistry, Chinese Academy of SciencesTel: 0086-10-62562894 ，82618423* ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Using ACE and NAC with oplsaa
[EMAIL PROTECTED] wrote: Appologies, two entries are required (the first is for ACE and the second is for NAC): [ dihedraltypes ] ; ijkl func coefficients CT C N CT_23 30.28798 -4.81160 -25.47638 0.0 0.0 0.0 For ACE (Sept2006) adapted from CT_2-N-C-CT_2 parameters with original comment=peptide - V1 changed to 2.3 CT_2 C N CT 3 30.28798 -4.81160 -25.47638 0.0 0.0 0.0 For NAC (Sept2006) adapted from CT_2-N-C-CT_2 parameters with original comment=peptide - V1 changed to 2.3 *** These entries look correct to me. As an unrelated point: I receive the users list as a coallated email, not as individual emails. Therfore I can't reply directly to an email and can't put a response in the same thread. That isn't ideal (eg. for situations like this where it would be nice for somebody searching later to find a next in thread). Is there a way to hack the subject line in order to get a message put into a thread without also having to get all the posts as individual emails? Thanks. No. Threading is not done by interpreting the contents of the subject line, but rather through the use of headers that aren't normally visible in mail readers without the user saying they want to see them. Digests break this. Mark ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bond-bond and bond-angle cross terms
Camilo Calderon wrote: Hi all! I am new to the GROMACS-world, and I am mystified. How do I implement the 3 body potentials advertised in sec. 4.2.8 and sec. 4.2.9 of the GROMACS 3.3 manual? Right now I have the following: [ cross_cross_bond ] ;ai aj funct r1e r2e krr numbers here [ cross_bond_angle ] ;ai aj ak funct r1e r2e r3e krt more numbers here when I grompp the topol.top, what I get is a Error, with a complaint invalid directive, and then a Fatal Error, with the complaint Incorrect number of parameters - found 5, expected 2 or 4. What is really tough about this is that I've been poring over the source code, trying to decypher what input format ought to be - there is nothing on this either in the Manual, or in the various lists! The contents of either gmxlib/ifunc.c or kernel/ifunc.c (sorry can't remember which it is) may help you work out how many parameters it needs - text search for CROSS, and then find the definition of the macro that is being used there. Can you give us more detail from the .top file and the error messages grompp returns? Mark ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] The molecule size
主月 ：） wrote: Hi: Two melt models were built for polyethylene (PE) and polyvinylmethylether (PVME) melt with PBC condition . The density of both melt model agree with experimenal value well.But when one check the radius of gyration (Rg) of them, both of them were too small to accept as follows. The Rg for PE (C1000) is just 28 angstrom. It means the infinite charaterastic ratio (Cinf) for the polymer is just about 2 which is much smaller than scatter experimental value about 7. The Rg for PVME (C44) melt is about 6.6 angstrom. It means the Cinf for the polymer is just 2.5 which is much smaller than scatter experimental value 8-10. Can these results be accepted? Is there any fault in force field? gromos96a Usually a garbage result as output means that you had either garbage as input, or garbage for the algorithm. Find a published article that describes a similar simulation and adapt their method suitably. Otherwise describe your method more thoroughly (e.g. how large was the box, what ensemble did you use, equilibration regime, etc.) and maybe someone has some judgement they can share with you. Mark ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
