Hi Cristina,
> > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS
> > = 0.0
> > Etot = -119235.7327 EKtot = 0.0000 EPtot =
> > -119235.7327
> > BOND = 120.1323 ANGLE = 762.7237 DIHED =
> > 3442.2867
> > 1-4 NB = 1372.0187 1-4 EEL = 15491.2504 VDWAALS =
> > 4621.6183
> > EELEC = -145045.7628 EHBOND = 0.0000 RESTRAINT
> > = 0.0000
> > Ewald error estimate: 0.4162E-03
> > --------------------------------------------------------------------
> ----------
> >
> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
> 0.000
> >
> =======================================================================
> ========
> > vlimit exceeded for step 2; vmax = 33.0050
> > vlimit exceeded for step 3; vmax = 25.9657
The energies look fine and very similar to other mutant which doesn't show
this. You may find that this is transient and you can ignore it, if it only
happens on the first few steps you might be okay. The best option though
would be to try running a short 100 step or so run and recording the
coordinates every step. Then you can look and see if anything looks strange.
It is also possible to put a print statement in the vlimit code to show
which atom is exceeding the limit.
Try
nstlim=100, ntwx=1, ntpr=1,
And watch it in VMD and see if you can see what is happening. Note the
vlimit default is 20 so the above numbers are fairly close to the limit
where they wouldn't show up.
> I do not see any major differences however, one is running and one is
> not.
When you say one is not, does it crash with an error? Or just give you
vlimits for the first few steps and then continue?
> The input file that I use is:
> > heat 1modnew pdb model
> > &cntrl
> > imin=0,irest=0,ntx=1,
> > nstlim=25000,dt=0.002,
> > ntc=2,ntf=2,
> > cut=11.0, ntb=1,
> > ntpr=500, ntwx=500,
> > ntt=3, gamma_ln=2.0,
> > tempi=0.0, temp0=300.0,
> > ntr=1,
> > restraint_wt=2.0,
> > nmropt=1,
> > restraintmask = '(:1-359)',
> > /
> > &wt TYPE='TEMP0', istep1=0, istep2=25000,
> > value1=0.1, value2=300.0, /
> > &wt TYPE='END' /
There may be something going wrong in the restraints. Note you probably
don't need the brackets in the expression above. Check that the number of
atoms you expect is being found. Running with NTPR=1 will also help you see
if the restraint energy suddenly shoots up.
> I checked the system after the minimization step and it looked fine. I
How long did you minimize for? Also did you have shake on when you did the
minimization? If you didn't then you will have H atoms at 'non-shake'
distances and then you are using this as a reference for your restraints
which means you will always get restraint forces due to shake trying to
reset the H atom positions. Just a guess but it is possible this is causing
issues. You could also try minimizing some more, what was the RMS and GMAX
forces at the end of the minimization? - Which atom did it list as having
the most force on it? - This is likely to be where any problems lie.
Good luck,
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
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Received on Mon Jun 21 2010 - 11:00:04 PDT
