[gmx-users] any help for PPPM?
Hi, For the past few days , we've been carrying out a simluation by using PPPM , for some reason we end up with some wired pressure tensors. Based on manual , it says it is not easy to calculate the full long-range virial tensor with PPPM correctly, but it is possible to obtain the trace. What confused us is that if one can get the trace right why couldn't get correct virials? We have done some literature searches , but until now still couldn't figure out why is it. So , can anyone point out why we have such an issue between PPPM and virial tensor caculation ? and can you give me a reference where I can learn more about? thanks in advance Kevin Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com___ 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] any help for PPPM?
feng chen wrote: Hi, For the past few days , we've been carrying out a simluation by using PPPM , for some reason we end up with some wired pressure tensors. Based on manual , it says it is not easy to calculate the full long-range virial tensor with PPPM correctly, but it is possible to obtain the trace. What confused us is that if one can get the trace right why couldn't get correct virials? We have done some literature searches , but until now still couldn't figure out why is it. So , can anyone point out why we have such an issue between PPPM and virial tensor caculation ? and can you give me a reference where I can learn more about? thanks in advance Kevin The implementation of PPPM in gromacs is ancient, it is based on work by Luty & Van Gunsteren, 1995 or so. In order to use pressure coupling one would have to update the code. Hunenberger has described how to do it, around 2000, but we haven't come around to implement it, largely because we've put much more effort into optimizing PME, even though some people maintain that PPPM is more efficient in principle. What it boils down to is that you're on your own when you want to use it. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] Re:realloc Error !
I have a complex protein which is predicted from cluspro server,I use it as a start structure,I want to know the complex will deformated to a new conformation which is NMR experiment result(it only include a fragment of protein).So I want to know the two protein interaction information by MD. I use energy minimize step to get optimize structure,but there Fmax always >1.So I don't know how to do! Otherwise,I got another error message in same situation: Fatal error: Box was shifted at least 10 times. Please see log-file. I also don't know how to understand it. Could you tell me reason?Thank you very much! > > Dear users: > > I simulate a large system which are 27062 atoms (include water),after mdrun > > hours,I receive a error message: > > Fatal error: > > realloc for grid->nra (-410897240 bytes, file nsgrid.c, line 159, grid->nra=0x0x > > 8cd3200) > > > > Could somebody tell me what wrong with it,what should I do? > > Thank you very much! > > Probably, equilibrate the system better. You'd need to tell us more > about what you're doing in order to get a better guess, however. > > 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] Re:realloc Error !
Qiang Zhong wrote: I have a complex protein which is predicted from cluspro server,I use it as a start structure,I want to know the complex will deformated to a new conformation which is NMR experiment result(it only include a fragment of protein).So I want to know the two protein interaction information by MD. I use energy minimize step to get optimize structure,but there Fmax always >1.So I don't know how to do! You need an adequately minimized structure, but you won't be able to get Fmax of zero. "Adequate" just means that later when you heat the system and do your equilibration run that things do not fall apart. Otherwise,I got another error message in same situation: Fatal error: Box was shifted at least 10 times. Please see log-file. When? During the minimization? What was different between when you got this error message and when you didn't? I also don't know how to understand it. Could you tell me reason?Thank you very much! Please be aware that in typed English, spaces are used after punctuation marks like commas, periods and interrogation marks (i.e. ',', '.', '?') in order to make the text easier to read. 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
