Dear Dr. Spoel, Initially I used a 100ns simulation with 0.002 time step. Then I tried a 10ns simulation with 0.0005 timestep and lower output frequency. I used -ac option and obtained the forward lifetime.
Regards, Apramita Reply to :Message: 2 Date: Fri, 7 Sep 2018 08:14:48 +0200 From: David van der Spoel <sp...@xray.bmc.uu.se> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Warning: correlations not long enough Message-ID: <ad407060-789d-bc24-354d-cbf089b8a...@xray.bmc.uu.se> Content-Type: text/plain; charset=windows-1252; format=flowed Den 2018-09-06 kl. 17:13, skrev Apramita Chand: > Dear All, > In my simulations ,I have a Peptide in aqueous solution with a cosolvent. > > For more number of hydrogen bonds like peptide water, water-water, there > are no warnings > > But for Peptide cosolvent, there are 315 hydrogen bonds and it does the acf > as 315/315... > > It shows warning: correlations not long enough > > My original time step was 0.002 and I changed it to 0.0005 and even lowered > the output frequency of coordinates > How long is the simulation? You do not have to store so often, may 50 fs is enough, but you may need a longer simulation. If 45 ps is a realistic correlation time you need at least some nanoseconds. And do not use the -life option, as is described in my old JPCB 110 pp. 4393-4398 (2006). > Doing so gave me a 80GB output file! > > Still the problem persists.. > > The lifetime that is output on the screen is 45 ps. > > Since it writes that the lower half of the correlation function was fitted > and then this is calculated, can I quote this lifetime? Is it accurate? > > > > Please help > > > Yours sincerely > Apramita > -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se ------------------------------ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.