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?
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.
