Dear David, Could you please more explain each term of the formula you said?
Formula=The number of atoms (N * 3)^2 times number of frames times 4 bytes Why square the number of atoms? Why 4 bytes? Thanks in advance > On 21 Jun 2016, at 09:39, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > >> On 21/06/16 08:11, Billy Williams-Noonan wrote: >> Sorry, the original post provides an example of the -dt flag with 100ps >> intervals. > You can calculate how much space you need by number of atoms (N * 3)^2 times > number of frames times 4 bytes. > > Do you select just your biomolecule? > >> >> On 21 June 2016 at 16:10, Billy Williams-Noonan < >> billy.williams-noo...@monash.edu> wrote: >> >>> Thank you for your reply. :) >>> >>> My main problem is with gmx covar which does not have a -skip flag. As >>> you can see from the OP I have tried the -dt flag with 250ps intervals. It >>> still crashes due to insufficient memory. It also crasses with 5000ps >>> intervals, giving me just 20ps of frames to work with for the whole >>> ensemble. >>> >>> Billy >>> >>> On 21 June 2016 at 16:00, David van der Spoel <sp...@xray.bmc.uu.se> >>> wrote: >>> >>>>> On 21/06/16 07:34, Billy Williams-Noonan wrote: >>>>> >>>>> Hi Gromacs Users, >>>>> >>>>> I am running g_mmpbsa.py to calculate the binding enthalpy of a cyclic >>>>> peptide in a drug target. At the same time I am trying to generate >>>>> ensemble estimates for entropy for the protein, ligand and complex. By >>>>> using these two variables I aim to get an idea of the Gibbs free energy >>>>> of >>>>> binding. >>>>> >>>>> My system for the complex and the protein is some 50,000 atoms large, >>>>> with just over 3000 atoms belonging to the proteins, and the rest of the >>>>> system is water and ions, to make up a physiological concentration of >>>>> NaCl. These are approximate estimates and not exact numbers. gmx covar >>>>> seems to keep crashing every time I try to use it to generate >>>>> eigenvectors >>>>> for the system. These are the commands I am using: >>>>> >>>>> >>>>> " gmx covar -f md.xtc -s md.tpr -v md.eigenvec.trr -av average.pdb >>>>> -ascii >>>>> covar -xpm covar -xpma covara -l covar -o md.eigenval.xvg -dt 100 -pbc >>>>> yes >>>>> << EOF >>>>> 0 >>>>> 0 >>>>> EOF " >>>>> >>>>> and: >>>>> >>>>> " gmx anaeig -v md.eigenvec.trr -f md.xtc -s md.tpr -entropy -temp 300 > >>>>> out.entropy.schlitter " >>>>> >>>>> >>>>> I have tried this on a local machine with 16GB of RAM and on a cluster >>>>> using one core and a node's worth of RAM (128GB). I do not have access >>>>> to >>>>> more RAM than this. Any ideas on how I can stop my calculation from >>>>> crashing due to insufficient memory? >>>> Use the -skip or -dt flags. >>>> >>>> >>>>> Kind regards, >>>>> >>>>> Billy >>>> >>>> -- >>>> 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 >>>> -- >>>> 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. >>> >>> >>> >>> -- >>> Billy Noonan* | *PhD Student *|* Bsci ( *Adv* ), IA Hon >>> >>> *LinkedIn Profile >>> <http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button> >>> **|* +61420 382 557 >>> >>> Monash Institute for Pharmaceutical Sciences ( *MIPS* ) >>> Royal Parade, Parkville, 3052 > > > -- > 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 > -- > 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.