Re: [gmx-users] mdrun error: There is no domain decomposition for x nodes that is compatible with the given box
On 5/6/15 7:26 AM, Mark Abraham wrote: On Wed, May 6, 2015 at 9:01 AM Seyed Mojtaba Rezaei Sani s.m.rezaeis...@gmail.com wrote: Dear Justin Thanks for your kind response. I didn't notice the point you mentioned. It seems that grompp doesn't care the difference betwen vdwq and vdw-q. however, I corrected the script. The error remains even in the case of choosing 2 nodes. The only way to have a successful run is a serial calculation. Then that's life (except that if your protein is non-spheroidal, you might have better luck with the long axis aligned to the z-axis). The domain decomposition code expects bonded interactions to be of shorter range than short-ranged non-bonded interactions, so will not produce a decomposition that has a bonded interaction that starts in one domain, crosses another domain, leaves by the opposite face, and reaches a third domain. This is implemented by setting a minimum size for domains based on many properties of the observed starting structure. There's a brief summary of these choices printed in every .log file. The use of couple-intramol triggers the generation of atypical interactions, that are implemented like bonds as far as the DD code knows, and for a protein those bonds are so much longer that they set a minimum size that means a decomposition is infeasible. AFAIK, FEP on a whole protein isn't going to work at all anyway. True. But is DOX isn't a protein; it's doxorubicin. There is no reason that I can think of that would cause DD to fail unless the box is unreasonably small. An extension of normal interactions out to 1.9 nm should be within normal limits if the box is of adequate size. Perhaps the OP can give us more information (linking the .log rather than trying to attach it) and describing the box size. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] mdrun error: There is no domain decomposition for x nodes that is compatible with the given box
Thank you Mark. As Justin suggested I increased the box size and now I can run the job on 4 machines. The old md.log file can be found here: https://www.dropbox.com/s/bbmqln6oqjyus0b/md.log?dl=0 My first choice for the box was a dodecahedron one with the option -d 1nm which now is increased to 2 nm. Thank you Justin for your useful help. On Wed, May 6, 2015 at 4:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/6/15 7:26 AM, Mark Abraham wrote: On Wed, May 6, 2015 at 9:01 AM Seyed Mojtaba Rezaei Sani s.m.rezaeis...@gmail.com wrote: Dear Justin Thanks for your kind response. I didn't notice the point you mentioned. It seems that grompp doesn't care the difference betwen vdwq and vdw-q. however, I corrected the script. The error remains even in the case of choosing 2 nodes. The only way to have a successful run is a serial calculation. Then that's life (except that if your protein is non-spheroidal, you might have better luck with the long axis aligned to the z-axis). The domain decomposition code expects bonded interactions to be of shorter range than short-ranged non-bonded interactions, so will not produce a decomposition that has a bonded interaction that starts in one domain, crosses another domain, leaves by the opposite face, and reaches a third domain. This is implemented by setting a minimum size for domains based on many properties of the observed starting structure. There's a brief summary of these choices printed in every .log file. The use of couple-intramol triggers the generation of atypical interactions, that are implemented like bonds as far as the DD code knows, and for a protein those bonds are so much longer that they set a minimum size that means a decomposition is infeasible. AFAIK, FEP on a whole protein isn't going to work at all anyway. True. But is DOX isn't a protein; it's doxorubicin. There is no reason that I can think of that would cause DD to fail unless the box is unreasonably small. An extension of normal interactions out to 1.9 nm should be within normal limits if the box is of adequate size. Perhaps the OP can give us more information (linking the .log rather than trying to attach it) and describing the box size. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- Seyed Mojtaba Rezaei Sani Institute for Research in Fundamental Sciences (IPM) School of Nano-Science Shahid Farbin Alley Shahid Lavasani st P.O. Box 19395-5531 Tehran, Iran Tel: +98 21 2310 (3069) -- 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.
[gmx-users] mdrun error: There is no domain decomposition for x nodes that is compatible with the given box
Dear gmx users, Perhaps my problem is a repetitive question in the forum but I couldn't find a trouble-shooter response for my case. I am running a stochastic dynamics calculation for a solution of doxorubicin. The following error occurs while the calculation runs: Fatal error: There is no domain decomposition for x nodes that is compatible with the given box and a minimum cell size of 1.9433 nm Change the number of nodes or mdrun option -rdd or -dds I have tried several numbers of nodes resulting in the same error. Here is the mdp file: integrator = sd nsteps = 100 dt = 0.002 nstenergy= 1000 nstlog = 5000 ; turn off trajectory writing nstxout = 0 nstvout = 0 ; cut-offs at 1nm rlist= 1.0 nstlist = 10 coulombtype = pme vdw-type = cut-off rvdw = 1.0 constraints = all-bonds ; set temperature to 300K tcoupl = v-rescale tc-grps = system tau-t= 0.2 ref-t= 300 ; and pressure to 1 bar pcoupl = parrinello-rahman ref-p= 1 compressibility = 4.5e-5 tau-p= 5 ; and set the free energy parameters free-energy = yes couple-moltype = DOX init-lambda = 0 ; these 'soft-core' parameters make sure we never get overlapping ; charges as lambda goes to 0 sc-power = 1 sc-sigma = 0.3 sc-alpha = 1.0 ; we still want the molecule to interact with itself at lambda=0 couple-intramol = no couple-lambda1 = vdwq couple-lambda0 = none foreign-lambda = 0 0.2 0.4 0.6 0.8 0.9 1 would you give me some hints? Thanks in advance. -- Seyed Mojtaba Rezaei Sani Institute for Research in Fundamental Sciences (IPM) School of Nano-Science Shahid Farbin Alley Shahid Lavasani st P.O. Box 19395-5531 Tehran, Iran Tel: +98 21 2310 (3069) -- 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.
Re: [gmx-users] mdrun error: There is no domain decomposition for x nodes that is compatible with the given box
On 5/5/15 8:48 AM, Seyed Mojtaba Rezaei Sani wrote: Dear gmx users, Perhaps my problem is a repetitive question in the forum but I couldn't find a trouble-shooter response for my case. I am running a stochastic dynamics calculation for a solution of doxorubicin. The following error occurs while the calculation runs: Fatal error: There is no domain decomposition for x nodes that is compatible with the given box and a minimum cell size of 1.9433 nm Change the number of nodes or mdrun option -rdd or -dds I have tried several numbers of nodes resulting in the same error. Here is the mdp file: integrator = sd nsteps = 100 dt = 0.002 nstenergy= 1000 nstlog = 5000 ; turn off trajectory writing nstxout = 0 nstvout = 0 ; cut-offs at 1nm rlist= 1.0 nstlist = 10 coulombtype = pme vdw-type = cut-off rvdw = 1.0 constraints = all-bonds ; set temperature to 300K tcoupl = v-rescale tc-grps = system tau-t= 0.2 ref-t= 300 ; and pressure to 1 bar pcoupl = parrinello-rahman ref-p= 1 compressibility = 4.5e-5 tau-p= 5 ; and set the free energy parameters free-energy = yes couple-moltype = DOX init-lambda = 0 ; these 'soft-core' parameters make sure we never get overlapping ; charges as lambda goes to 0 sc-power = 1 sc-sigma = 0.3 sc-alpha = 1.0 ; we still want the molecule to interact with itself at lambda=0 couple-intramol = no This is what triggers the error. Note from the manual, for couple-intramol = no: All intra-molecular non-bonded interactions for moleculetype couple-moltype are replaced by exclusions and explicit pair interactions. In this manner the decoupled state of the molecule corresponds to the proper vacuum state without periodicity effects. The added exclusions and pairs require larger DD cells to be constructed because these bonded interactions occur over larger distances than normal. This limits the size of the DD cells and hence how many processors/cores you can use. You haven't said how many you're trying to use, but the solution is simply to use fewer. couple-lambda1 = vdwq The option is vdw-q but I don't know if grompp magically translates it. Just check. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
