Dear Peter, I appreciate your explanation :)
Regards, Shima ----- Original Message ----- From: Peter C. Lai <p...@uab.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com> Cc: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Saturday, June 30, 2012 8:57 PM Subject: Re: [gmx-users] Berger lipid 323 is proper for a higher melting point lipid like DPPC. You can easily simulate POPC at 300, and many other people have done so. In fact I received criticism from a reviewer as to why I picked an elevated temperature of 310, despite the fact that 310 is physiological temperature (to make some experimentalist reviewers happy). Some early rhodopsin runs were done at 310 and I'm pretty sure that was included as a reference in the rationale for the elevated temperature (besides the standard "310 is well above the solid phase transition temperature for POPC" line). Neither the g_membed authors nor Klauda run POPC above 310K if I remember correctly. On 2012-06-30 07:33:38AM -0700, Shima Arasteh wrote: > Dear Peter, > Thanks for your link and the article. > I'd like to know more about your paper. You've mentioned in it that the > temperature of POPC equilibrated, is 310 K. As I saw in Justin's tutorial , > 323 K is proper, however it was a different system simulated and also many > parameters are not the same as your system . Would you telling me about the > reason of 310 K? > > Thanks in advance > > > Sincerely, > Shima > > > ----- Original Message ----- > From: Peter C. Lai <p...@uab.edu> > To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS > users <gmx-users@gromacs.org> > Cc: > Sent: Friday, June 29, 2012 2:54 PM > Subject: Re: [gmx-users] Berger lipid > > yes > http://www.frontiersin.org/Bioinformatics_and_Computational_Biology/10.3389/fgene.2012.00061/abstract > > The files are here: > http://uab.hyperfine.info/~pcl/files/popc36/ > > On 2012-06-28 09:58:26PM -0700, Shima Arasteh wrote: > > Yes, I remember now...................you are right :) But I didn't know > > the linked you sent me, was your own output! However I wanted to know if > > it is necessary to produce the .itp file on my own or not. > > > > I still have this link, so will cite to you. It would be a good idea to see > > its package in lipidbook too. > > Thanks Peter > > > > > > > > > > Sincerely, > > Shima > > > > > > ________________________________ > > From: Peter Lai <p...@uab.edu> > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Sent: Friday, June 29, 2012 7:14 AM > > Subject: RE: [gmx-users] Berger lipid > > > > Uh didn't we go through all of this like more than a month ago? I published > > a paper using C36 POPC and even a linked to my popc.itp for it on this > > list... > > > > Of course Shima is welcome to pdb2gmx his own POPC, which I am fairly > > certain will result in an identical file... > > > > Lipidbook seems to only have C36 POPE. I guess maybe I will upload ours. > > ________________________________________ > > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on > > behalf of Justin A. Lemkul [jalem...@vt.edu] > > Sent: Thursday, June 28, 2012 7:56 PM > > To: Discussion list for GROMACS users > > Subject: Re: [gmx-users] Berger lipid > > > > On 6/28/12 8:54 PM, Shima Arasteh wrote: > > > Yes, I know that as studied the Kalp15 tutorial. > > > Sorry, the last question :) > > > : > > > > > > DO I need to run pdb2gmx to get the top file of POPC in CHARMM36? Is > > >it ok? Because I see that POPC.itp is also required for simulation of > > >protein in bilayer. > > > > > > > You need a topology of some sort. It depends on what parameters you have on > > hand. If you do not have popc.itp from anywhere, then you need to generate > > it > > somehow. If it is present in the .rtp file for CHARMM36 that you have, > > then you > > can run pdb2gmx on it. > > > > -Justin > > > > -- > > ======================================== > > > > Justin A. Lemkul, Ph.D. > > Research Scientist > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Only plain text messages are allowed! > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Only plain text messages are allowed! > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Only plain text messages are allowed! > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > ================================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
