It seems you have made the fix correctly. The fix I suggested was
incomplete, in that it should read:
if (((objcode == ANGL_CODE || objcode == NMR3_CODE) && ispresent[2] == 0) ||
(objcode == CMAP_CODE && ispresent[4] == 0)) {
But, unless you have NMR3 (3-point NMR restraint) terms in your system this
is not your problem. Simmerling is finding that the fix I suggested goes a
long way to fixing his problem but something else is still causing
trouble. I'll keep you posted on what I can find. Meanwhile, can you send
me your system and run conditions in a direct email?
Dave
On Fri, Dec 11, 2020 at 8:43 AM Женя Елизарова <zheneliz147.gmail.com>
wrote:
> I've tried to change the code as you suggested, but still, this error
> occurred. Probably, I need to change somewhere else?
> In the attachment, there is a file, that I changed so you can check it in
> case I did something wrong.
>
> Best wishes,
> Evgenia Elizarova
>
> ср, 9 дек. 2020 г. в 11:50, David Cerutti <dscerutti.gmail.com>:
>
> > I did some investigations on a separate topic, and systems set up with
> > ff19SB may fail for reasons relating to a bug in the bond work unit
> > allocation when CMAPs are involved. I will be patching the code ASAP,
> but
> > in lieu of the patch you can go into ${AMBERHOME}/src/pmemd/src/cuda/ and
> > access the file bondRemap.cpp. This is a problem with how the host sets
> up
> > the tables for the GPU to execute, but the fix is to look at or about
> line
> > 395 and change the code block starting there to:
> >
> > if (objcode == ANGL_CODE || objcode == NMR3_CODE || objcode ==
> CMAP_CODE)
> > {
> > if ((objcode == ANGL_CODE && ispresent[2] == 0) ||
> > (objcode == CMAP_CODE && ispresent[4] == 0)) {
> > bw->atomList[nunitatom] = p1atm[objID];
> > nunitatom++;
> > }
> > if (unitMapCounts == NULL) {
> > itmp = unitMap->data;
> > itmp[p1atm[objID]] = unitID;
> > }
> > else {
> > unitMap->map[p1atm[objID]][unitMapCounts->data[p1atm[objID]]] =
> > unitID;
> > unitMapCounts->data[p1atm[objID]] += 1;
> > }
> > }
> >
> > The crucial thing is that "if (ispresent[2] == 0)" changes to either of
> two
> > pairs of conditions, involving the objcode as well as the array tracking
> > whether an atom in the object is already present in the work unit's
> import
> > group. I have already verified that this is a bug and that fixing it
> > solves a similar problem in one of the Simmerling lab's systems, where it
> > would cause failures like what you are seeing after 35k, 55k, or even
> 100k
> > steps. But, if you can modify your own code and re-run your test to
> > confirm that this solves your problem, that would be ideal.
> >
> > Thanks,
> >
> > Dave
> >
> >
> > On Fri, Dec 4, 2020 at 11:13 AM David A Case <david.case.rutgers.edu>
> > wrote:
> >
> > > On Mon, Nov 30, 2020, Женя Елизарова wrote:
> > > >
> > > >I tried different force fields for protein. It occured that the
> problem
> > > (an
> > > >error "cpubuffer..") was with ff19SB force field. Calculations with
> > > another
> > > >types of force fields (14,99) are more stable. Does it mean that i
> can't
> > > >use that force field? Or maybe you know how to fix it?
> > >
> > > One thing worth trying: get you system well-equilibrated with ff14SB,
> > > then switch prmtop files to one for ff19SB, and continue the simulation
> > > after (potential) bad interactions have been removed. It would be of
> > > interest to know if the ff19SB-related problems still show up.
> > >
> > > ....regards...dac
> > >
> > >
> > > _______________________________________________
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> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> >
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Received on Fri Dec 11 2020 - 07:00:03 PST
