On Thu, Oct 30, 2014 at 12:30 PM, Ioanna Styliari <pax...@nottingham.ac.uk> wrote: > Thank you both for your prompt replies. > > Dr Vitaly Chaban: Is there any way of evaluating how many nodes are needed or > is it just by a trial-error approach?
If your number of cores gives an error, try another number of cores. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН > Justin: Although 1fs works, I was aiming for 2fs steps in the MD but it > crashes. I was thinking to run the first 2ns with 1fs and then try to > continue it with 2fs onwards to see what happens, but it crashed at 700ps of > my MD. I am using GROMOS96 53a6. > My equilibration "concern" regards the system: should it be equilibrated as a > whole or should I equilibrate one part of it at a time, keeping the others > fixed? (which was a suggestion I had but I am unsure how to do it) > > Again, thank you > > Ioanna > > _ _ _ _ _ _ _ _ _ _ _ _ _ > Miss Ioanna Danai Styliari > PhD Candidate > Centre for Doctoral Training in > Targeted Therapeutics and Formulation Sciences > School of Pharmacy > University of Nottingham > Nottingham > NG7 2RD > Email: pax...@nottingham.ac.uk > Telephone: 0044 (0) 74 49890176 > > > 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 legislation. > > > > > > > > > > -- > 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. -- 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.
