AMBER Archive (2009)

Subject: RE: [AMBER] vlimit

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Oct 28 2009 - 16:29:21 CDT

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
>
>
>
>
>
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> AMBER_at_ambermd.org
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