Thanks for the reply. Since I need to study the effect of beta-hairpin turn design on protein folding . I thought that first unfolding and then refolding would give the change in folding time. As you told that to do such a task would require large computational power. Is there any other method in MDS that could be used ??
On Wed, Jan 4, 2012 at 10:52 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 4/01/2012 12:35 PM, bharat gupta wrote: > >> Thanks for all your replies. I want to know this can be done in gromacs >> or not - using REMD with structure based models generated from SMOG server >> to study protein folding and unfolding ??. >> > > Well, it can be done, but you probably don't have enough computer to fold > a 230 residue protein at atomistic resolution (or maybe even > coarse-grained). > > > Also, I have a question about how to determine the exchange probablities >> for a particular REMD experiment and also how many replicas do we need to >> consider, does that depend on the temperature list generated from the >> T_REMD server?? >> > > There's a significant literature on these subjects. I suggest you read > some of it. Short answer: pick the highest temperature according to the > size of the largest barrier you expect to cross (good luck guessing that), > have around 20% exchange acceptance, and be prepared to observe where the > replica-flow bottle necks are and to iteratively refine you temperatures. > > Mark > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com
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