2017-11-08 23:53 GMT-07:00 <[email protected]>: > Hi, > > I am trying to use csg_fmatch to perform force matching for a DPPC lipid > system. A single lipid has 12 beads. I obtained the reference interactions > for all the bonded and non-bonded interactions using csg_stat. > The profile of these interactions look fine to be. I determine the min and > max of these interactions from the reference distributions. The fmatch.xml > file is attached. > I use the following for force matching - csg_fmatch --top dppc40.tpr --trj > dppc40.trr --cg ../dppc.xml --options fmatch.xml > > I get the following error - > an error occurred: > std::bad_alloc > ----------------------------------------------------------------------------------- > I have 1536 beads in 128 molecules for the coarsegraining > trr version: GMX_trn_file (single precision) > Reading frame 0 time 0.000 > Number of spline functions for the interaction NC3-PO4:62 > Number of spline functions for the interaction PO4-GL1:62 > Number of spline functions for the interaction PO4-GL2:62 > Number of spline functions for the interaction GL1-C1A:62 > Number of spline functions for the interaction GL2-C1B:62 > Number of spline functions for the interaction C1A-C2A:62 > Number of spline functions for the interaction C2A-C3A:62 > Number of spline functions for the interaction C3A-C4A:62 > Number of spline functions for the interaction C1B-C2B:62 > Number of spline functions for the interaction C2B-C3B:62 > Number of spline functions for the interaction C3B-C4B:62 > Number of spline functions for the interaction NC3-PO4-GL1:440 > Number of spline functions for the interaction NC3-PO4-GL2:440 > Number of spline functions for the interaction PO4-GL1-C1A:440 > Number of spline functions for the interaction PO4-GL2-C1B:440 > Number of spline functions for the interaction GL1-C1A-C2A:440 > Number of spline functions for the interaction GL2-C1B-C2B:440 > Number of spline functions for the interaction C1A-C2A-C3A:440 > Number of spline functions for the interaction C1B-C2B-C3B:440 > Number of spline functions for the interaction C2B-C3B-C4B:440 > Number of spline functions for the interaction NC3-NC3:330 > Number of spline functions for the interaction NC3-C1A:330 > Number of spline functions for the interaction NC3-C2A:330 > Number of spline functions for the interaction NC3-C3A:330 > Number of spline functions for the interaction NC3-C4A:330 > Number of spline functions for the interaction NC3-C1B:330 > Number of spline functions for the interaction NC3-C2B:330 > Number of spline functions for the interaction NC3-C3B:330 > Number of spline functions for the interaction NC3-C4B:330 > Number of spline functions for the interaction PO4-C2A:330 > Number of spline functions for the interaction PO4-C3A:330 > Number of spline functions for the interaction PO4-C4A:330 > Number of spline functions for the interaction PO4-PO4:330 > Number of spline functions for the interaction PO4-C2A:330 > Number of spline functions for the interaction PO4-C3A:330 > Number of spline functions for the interaction PO4-C4A:330 > Number of spline functions for the interaction PO4-C2B:330 > Number of spline functions for the interaction PO4-C3B:330 > Number of spline functions for the interaction PO4-C4B:330 > Number of spline functions for the interaction GL1-GL1:330 > Number of spline functions for the interaction GL1-C3A:330 > Number of spline functions for the interaction GL1-C4A:330 > Number of spline functions for the interaction GL1-C3B:330 > Number of spline functions for the interaction GL1-C4B:330 > Number of spline functions for the interaction GL1-C1B:330 > Number of spline functions for the interaction GL1-GL2:330 > Number of spline functions for the interaction GL1-C2B:330 > Number of spline functions for the interaction GL2-GL2:330 > Number of spline functions for the interaction GL2-C3B:330 > Number of spline functions for the interaction GL2-C4B:330 > Number of spline functions for the interaction GL2-C1A:330 > Number of spline functions for the interaction GL2-C2A:330 > Number of spline functions for the interaction GL2-C3A:330 > Number of spline functions for the interaction GL2-C4A:330 > Number of spline functions for the interaction C1A-C1A:330 > Number of spline functions for the interaction C1A-C4A:330 > Number of spline functions for the interaction C1A-NC3:330 > Number of spline functions for the interaction C1A-GL2:330 > Number of spline functions for the interaction C1A-C1B:330 > Number of spline functions for the interaction C1A-C2B:330 > Number of spline functions for the interaction C1A-C4B:330 > Number of spline functions for the interaction C2A-C2A:330 > Number of spline functions for the interaction C2A-PO4:330 > Number of spline functions for the interaction C2A-NC3:330 > Number of spline functions for the interaction C2A-GL2:330 > Number of spline functions for the interaction C2A-C1B:330 > Number of spline functions for the interaction C2A-C2B:330 > Number of spline functions for the interaction C2A-C3B:330 > Number of spline functions for the interaction C2A-C4B:330 > Number of spline functions for the interaction C3A-C3A:330 > Number of spline functions for the interaction C3A-GL1:330 > Number of spline functions for the interaction C3A-PO4:330 > Number of spline functions for the interaction C3A-NC3:330 > Number of spline functions for the interaction C3A-GL2:330 > Number of spline functions for the interaction C3A-C1B:330 > Number of spline functions for the interaction C3A-C2B:330 > Number of spline functions for the interaction C3A-C3B:330 > Number of spline functions for the interaction C3A-C4B:330 > Number of spline functions for the interaction C4A-C4A:330 > Number of spline functions for the interaction C4A-C1A:330 > Number of spline functions for the interaction C4A-GL1:330 > Number of spline functions for the interaction C4A-PO4:330 > Number of spline functions for the interaction C4A-NC3:330 > Number of spline functions for the interaction C4A-C1B:330 > Number of spline functions for the interaction C4A-C2B:330 > Number of spline functions for the interaction C4A-C3B:330 > Number of spline functions for the interaction C4A-C4B:330 > Number of spline functions for the interaction C4A-GL2:330 > > You are using VOTCA! > > hey, somebody wants to forcematch! > > Using constrained Least Squares! > > an error occurred: > std::bad_alloc > ------------------------------------------------------------------------------------------- > > Can you please tell me where the mistake is ? Is it a memory problem ? My guess is that you ran out of memory. If you search the mailing list there are a couple of way to get around that, but most likely you will need to decrease <frames_per_block> value.
Christoph > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
