Hello,
I was saying that nscm would automatically remove COM translations, so the
system translating out of bounds wouldn't happen. This would only happen if
you had 2 species that were not bonded to one another (such as mobile
ions). You should not have any mobile ions in implicit solvent
calculations, anyway (only ions that are chemically relevant). You can use
saltcon to simulate the effects of mobile ions.
You should be able to figure out which atom is straying out of bounds based
on its location in the restart file. This will let you know where your
problem is. However, you should take out the Na+ ions and simulate your
system without them.
Lastly, if 2 parts of your system are not bonded and are drifiting away from
one another causing this problem, you have one of 2 options: simulate them
separately if they really don't interact, or impose a restraint to prevent
them from drifting too far away.
Hope this helps,
Jason
On Thu, Jul 22, 2010 at 9:42 AM, nicholus bhattacharjee <
nicholusbhattacharjee.gmail.com> wrote:
> Dear Jason,
> I do have mobile ions Na+ in my system. But looking at the
> trajectory file in vmd I dont think it is the Na+ ions. You asked me to use
> nscm. But it has the default value of 1000 and I have not changed. Then
> also
> looking at the trajectory in vmd shows that some residues are drifting..I
> dont know the reason.
>
> On Thu, Jul 22, 2010 at 5:36 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > Why do you have coordinates that are becoming too large for the fixed
> > format
> > restart file? Do you have mobile ions included? The COM translations
> > should be removed every nscm steps, so a small species not bonded to
> > anything must be drifting too far away, in which case I don't think it
> > should be part of your system at all. You can check your mdcrd file to
> see
> > which part is drifting too far away.
> >
> > Good luck!
> > Jason
> >
> > On Thu, Jul 22, 2010 at 7:41 AM, nicholus bhattacharjee <
> > nicholusbhattacharjee.gmail.com> wrote:
> >
> > > Dear Jason,
> > > I have just checked AMBER 10 manual. nxto=0 is no
> > loger
> > > supported with that. so what should I do.
> > >
> > > On Wed, Jul 21, 2010 at 12:33 PM, Jason Swails <jason.swails.gmail.com
> > > >wrote:
> > >
> > > > Hello,
> > > >
> > > > You do not need to create a cpin file from a cprestrt, the cprestrt
> > will
> > > > work just as well. As for the ambpdb error, does your restart file
> > have
> > > any
> > > > ********* entries from something migrating too far? How does the
> > restart
> > > > file look when you visualize it? ambpdb is failing on a floating
> point
> > > read,
> > > > so i'm guessing it's a problem with a coordinate.
> > > >
> > > > Visualizing will probably help you diagnose the problem.
> > > >
> > > > Good luck!
> > > > Jason
> > > >
> > > > --
> > > > Jason Swails
> > > > Quantum Theory Project,
> > > > University of Florida
> > > > Ph.D. Graduate Student
> > > > 352-392-4032
> > > >
> > > > On Jul 21, 2010, at 9:37 AM, nicholus bhattacharjee <
> > > > nicholusbhattacharjee.gmail.com> wrote:
> > > >
> > > > > Dear Jason,
> > > > > Thank you for your kind help. I have some other
> > > > problems
> > > > > also. As you can see from my earlier I am running 10 nano seconds
> > > > constant
> > > > > pH simulation in two batches of 5 nano seconds each. Now when the 5
> > > nano
> > > > > second run is over I am able to generate the properties (like rmsd,
> > > > trajout)
> > > > > from the trajectory file. But both my output files csprestrt and
> > > prod.rts
> > > > > files are corrupted for example
> > > > >
> > > > > if I do
> > > > >
> > > > > $ ambpdb -p prmtop <prod.rst> x.pdb
> > > > >
> > > > > its giving error msg
> > > > >
> > > > > | New format PARM file being parsed.
> > > > > | Version = 1.000 Date = 07/06/10 Time = 17:54:02
> > > > > At line 624 of file _ambpdb.f (unit = 5, file = 'stdin')
> > > > > Fortran runtime error: Bad value during floating point read
> > > > >
> > > > > I am unable to understand what is the problem. My prod.out file is
> > > giving
> > > > > the analysis of the whole trajectory. Please help...
> > > > >
> > > > > On Mon, Jul 12, 2010 at 10:04 AM, Jason Swails <
> > jason.swails.gmail.com
> > > > >wrote:
> > > > >
> > > > >> Hello,
> > > > >>
> > > > >> The cprestrt looks quite strange... However, this step described
> in
> > > the
> > > > >> manual is only necessary if you feel the need to get rid of all
> the
> > > > >> extraneous zeroes that crop up because you're not titrating the
> > > maximum
> > > > >> number of residues (50). sander simply dumps the contents of the
> > > whole
> > > > >> &cnstph namelist to the cprestrt file, then reads the contents of
> > the
> > > > >> &cnstph namelist when it reads the cpin file. Therefore, you can
> > just
> > > > use
> > > > >> the cprestrt as the cpin file directly without any modification.
> > > > >>
> > > > >> Good luck!
> > > > >> Jason
> > > > >>
> > > > >> On Mon, Jul 12, 2010 at 12:23 AM, nicholus bhattacharjee <
> > > > >> nicholusbhattacharjee.gmail.com> wrote:
> > > > >>
> > > > >>> Dear community,
> > > > >>> I am running a constant pH MD of 10 nano
> > > seconds
> > > > >> in
> > > > >>> a remote cluster. Since there is a cut of time of 72 hrs for user
> I
> > > > have
> > > > >> to
> > > > >>> break the simulation into two parts of 5 ns each. Now after the
> > first
> > > 5
> > > > >> ns
> > > > >>> simulation is over I have go cprestrt file from the simulation.
> > > > According
> > > > >>> to
> > > > >>> the manual I have to conver this cprestrt file to cpin2 file with
> > the
> > > > >>> following command
> > > > >>>
> > > > >>> $ cpintil.pl cprestrt > cpin2
> > > > >>>
> > > > >>>
> > > > >>> But it is showing the following errors
> > > > >>>
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in numeric lt (<) at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 238.
> > > > >>> Use of uninitialized value in array dereference at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 186.
> > > > >>> Can't call method "AtomCount" on an undefined value at
> > > > >>> /usr/local/amber9/exe/CPin.pm line 61.
> > > > >>>
> > > > >>>
> > > > >>> I am unable to understand what to do. Please help. I am attaching
> > the
> > > > >>> cprestrt file.
> > > > >>>
> > > > >>> --
> > > > >>> Nicholus Bhattacharjee
> > > > >>> PhD Scholar
> > > > >>> Department of Chemistry
> > > > >>> University of Delhi
> > > > >>> Delhi-110007 (INDIA)
> > > > >>> Phone: 9873098743(M)
> > > > >>>
> > > > >>> _______________________________________________
> > > > >>> AMBER mailing list
> > > > >>> AMBER.ambermd.org
> > > > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > > > >>>
> > > > >>>
> > > > >>
> > > > >>
> > > > >> --
> > > > >> Jason M. Swails
> > > > >> Quantum Theory Project,
> > > > >> University of Florida
> > > > >> Ph.D. Graduate Student
> > > > >> 352-392-4032
> > > > >> _______________________________________________
> > > > >> AMBER mailing list
> > > > >> AMBER.ambermd.org
> > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > >>
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Nicholus Bhattacharjee
> > > > > PhD Scholar
> > > > > Department of Chemistry
> > > > > University of Delhi
> > > > > Delhi-110007 (INDIA)
> > > > > Phone: 9873098743(M)
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Nicholus Bhattacharjee
> > > PhD Scholar
> > > Department of Chemistry
> > > University of Delhi
> > > Delhi-110007 (INDIA)
> > > Phone: 9873098743(M)
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 22 2010 - 07:30:08 PDT
