AMBER Archive (2009)

Subject: RE: [AMBER] vlimit

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Oct 28 2009 - 17:35:15 CDT

Hi Taufi,

Nothing strikes me as wrong here. The GMAX looks okay. Your bond energy is
maybe a little high but you have a lot of atoms so this is probably okay.

I would focus on running a few hundred steps of dynamics with ntpr=1 and
ntwx=1 and then look closely at the trajectory and see if you can see what
goes wrong.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Taufik Al-Sarraj
> Sent: Wednesday, October 28, 2009 3:03 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] vlimit
>
> Thank you Ross, i like the last suggestion about using the minimized
> structure as a reference and not the initial (very first) structure.
>
> sysdmin1/2.out are attached
>
> Ross Walker wrote:
> > Hi Taufi,
> >
> > Can you post the output from your two minimizations. Chances are your
> > initial structure is strained in some way. It may not be overlapping
> atoms,
> > it may be a very strained bond etc. Looking at the energy terms in
> the
> > minimization output will help identify the problem. It will also help
> to set
> > ntpr=1 so you get more details.
> >
> > For the heating try setting nstlim=50, ntpr=1 and ntwx=1. This will
> save the
> > coordinates on every step. Then you can look at it in something like
> VMD and
> > see what is initiating the blow up.
> >
> > Also for the heating try reducing the restraint weight to 1.0 and
> giving the
> > -ref as the same as the inpcrd file, I.e. the minimized structure.
> >
> > Good luck,
> > Ross
> >
> >
> >> -----Original Message-----
> >> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org]
> On
> >> Behalf Of Taufik Al-Sarraj
> >> Sent: Wednesday, October 28, 2009 2:17 PM
> >> To: AMBER Mailing List
> >> Subject: [AMBER] vlimit
> >>
> >> Hi,
> >> a molecular dynamics simulation just crashed giving me an error
> >> vlimit exceeded for step 4; vmax = 41.1136
> >> vlimit exceeded for step 5; vmax = 154.8294
> >>
> >> based on previous posts this can either be due to an atom with mass
> 0
> >> (zero) or two overlapping atoms
> >> my system is a little large (144000 atoms) so i cannot attach the
> >> prmtop
> >> or inpcrd files
> >>
> >> i ran two minimizations and they ran to completion without errors
> >>
> >> min1
> >>
> >> System minimization -everything fixed except water and Na+
> >>
> >> &cntrl
> >> imin = 1,
> >> maxcyc = 1000,
> >> ncyc = 500,
> >> ntb = 1,
> >> ntr = 1,
> >> iwrap = 1,
> >> cut = 8
> >> /
> >> Hold the Surface-linker-DNA fixed
> >> 10.0
> >> RES 1 41
> >> END
> >> END
> >>
> >>
> >> Min2
> >> System minimization -only the surface is fixed
> >>
> >> &cntrl
> >> imin = 1,
> >> maxcyc = 10000,
> >> ncyc = 5000,
> >> ntb = 1,
> >> ntr = 1,
> >> restraint_wt=20.0,
> >> restraintmask=':2',
> >> iwrap = 1,
> >> cut = 8
> >> /
> >>
> >> however when i try to run heat1 i get the vlimit error
> >>
> >> Heating from 0 to 200K -Molecular dynamics 20ps
> >> &cntrl
> >> imin = 0,
> >> irest = 0,
> >> ntx = 1,
> >> ntr = 1,
> >> nstlim = 10000,
> >> dt = 0.002,
> >> ntc = 2,
> >> ntf = 2,
> >> ntt = 3,
> >> gamma_ln = 1.0,
> >> tempi = 0.0,
> >> temp0 = 200.0,
> >> ntpr = 200,
> >> ntwx = 500,
> >> ntwr = 1000,
> >> ntb = 1,
> >> restraint_wt = 10.0,
> >> restraintmask = ':1-41',
> >> cut = 8.0
> >> /
> >>
> >> i looked the *.prmtop file, i don't have any mass = 0, i do have
> some
> >> LJ
> >> constants equal to zero but i hope these are for the water hydrogens
> >>
> >> i also tried ptraj sys.prmtop script
> >>
> >> script =
> >> {
> >> trajin sysdmin2.rst
> >> checkoverlap 0.95
> >> }
> >>
> >> but no atoms were found
> >>
> >> if i run the heat1 script with the following restraintmask = ':2'
> the
> >> simulation runs to completion with no errors!
> >>
> >> i have a couple of questions:
> >> Are there other reasons that can cause a velocity error that i have
> >> overlooked?
> >>
> >> if i set vlimit to say 20, wouldn't this prevent the simulation from
> >> crashing? if two atoms are too close, their velocity will be scaled
> >> according to the vlimit value, and in few (hundred) steps the two
> atoms
> >> will no longer overlap and the simulation will continue to run..
> >>
> >> Thanks,
> >> Taufik
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER_at_ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >

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