Got it, thanks very much David! :)
-----Original Message----- From: gmx-users-boun...@gromacs.org on behalf of David van der Spoel Sent: Sun 12/26/2010 5:55 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Replicating an experiment On 12/25/10 6:37 PM, NG HUI WEN wrote: > Thank you David for your prompt and useful reply :) I am in fact simulating > a membrane protein. > > It's good to know I can use the "generate-new-starting-velocity" method. But, > do you mind to elaborate a bit more what you mean by "if you simulate long > enough"? > > I would like to try your suggestion of picking a random structure from an > elevated temperature simulation. Can I achieve that by taking my existing > membrane protein system, > 1) pass it through grompp with a new mdp (with higher temperature) to produce > a new .tpr file > 2) simulate the system for a period (perhaps 1 ns) > 3) take any frame / final structure > 4) pass it through grompp again (with original mdp with temperature 300K, > gen_seed = -1) to produce the .tpr file for my replicate? > Yes that is what I meant. Of course you should check that your protein is not unfolding, or you membrane going into the wrong phase. > Thanks very much indeed!! > > ________________________________ > > From: gmx-users-boun...@gromacs.org on behalf of David van der Spoel > Sent: Sat 12/25/2010 10:28 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Replicating an experiment > > > > On 2010-12-25 15.05, NG HUI WEN wrote: >> Dear all, >> Merry Xmas! I have a very quick question here which i'd like to pick >> your brain on, would really appreciate a reply. >> I am planning to replicate an experiment that I have carried out. Just >> wondering what is the best way to do it? I am thinking of changing the >> starting velocity of my system by setting a random number e.g 23412445 >> etc in the gen_seed section as below, not sure if it is meaningful to do so? >> gen_vel = yes >> gen_temp = 300.0 >> gen_seed = random number >> Thank you for your input! > That will work fine, if you simulate long enough. Consider that the > starting structure may also influence how different your results will > be, e.g. for a protein in water. For liquids there is no such problem. > You can do a simulation and slightly elevated temperature and pick > structures from that with a different random seed, in order to randomize > your simulations even more. >> HW >> << >> >> This message and any attachment are intended solely for the addressee >> and may contain confidential information. If you have received this >> message in error, please send it back to me, and immediately delete it. >> Please do not use, copy or disclose the information contained in this >> message or in any attachment. Any views or opinions expressed by the >> author of this email do not necessarily reflect the views of the >> University of Nottingham. >> >> This message has been checked for viruses but the contents of an >> attachment may still contain software viruses which could damage your >> computer system: you are advised to perform your own checks. Email >> communications with the University of Nottingham may be monitored as >> permitted by UK& Malaysia legislation. >> >> >> >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell& Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se<http://folding.bmc.uu.se/> > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > 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 > > > << This message and any attachment are intended solely for the addressee and > may contain confidential information. If you have received this message in > error, please send it back to me, and immediately delete it. Please do not > use, copy or disclose the information contained in this message or in any > attachment. Any views or opinions expressed by the author of this email do > not necessarily reflect the views of the University of Nottingham. > > This message has been checked for viruses but the contents of an attachment > may still contain software viruses which could damage your computer system: > you are advised to perform your own checks. Email communications with the > University of Nottingham may be monitored as permitted by UK& Malaysia > legislation.>> > -- David. ________________________________________________________________________ David van der Spoel, PhD, Professor of Biology 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 sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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 << This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK & Malaysia legislation. >>
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