Dear AMBER users,
I have a question about vlimit. I have a system which is a methane
molecule with 3 dummy atoms connected to one of the hydrogen atom. I am
using this system to transform the methane to ethane molecule in water. I
have set only the nonbounded terms to be zero for the dummy atoms. The
simulation in gas phase went well. Now I am doing the same simulation in
water.
I have minimised the structure, and now I am trying to equilibrate the
system. The first phase I am doing is to heat it from 0 to 300 K in const.
volume. Here is the input file:
---------------------
Equilibration 1 - 20 ps, const vol. at lambda=0, k=6
&cntrl
imin=0,
ntx=1, irest=0,
ntpr=250,ntwr=1000,ntwx=250,
ntc=2, ntf=2, ntb=1, cut=6,
igb=0,
ntr=0,
nstlim=10000, dt=0.002, nscm=1000,
ntt = 3, gamma_ln=1.0, tempi=0.0, temp0=300.0,
icfe=1, clambda=0, klambda=6
/
----------------------
When I run sander, this gives a vlimit error as follows:
------------------------------------------------------------------------------
NSTEP = 250 TIME(PS) = 0.500 TEMP(K) = 116.80 PRESS = 0.0
Etot = -1782.8656 EKtot = 131.6075 EPtot = -1914.4730
BOND = 2.0551 ANGLE = 1.1080 DIHED = 0.0766
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 323.7974
EELEC = -2241.5100 EHBOND = 0.0000 RESTRAINT = 0.0000
DV/DL = 358.9765
Ewald error estimate: 0.4521E-03
------------------------------------------------------------------------------
vlimit exceeded for step 449 ; vmax = 22.7985467880131
vlimit exceeded for step 450 ; vmax = 25.8151633086237
vlimit exceeded for step 451 ; vmax = 34.9984252750174
vlimit exceeded for step 452 ; vmax = 20.3554699110933
vlimit exceeded for step 453 ; vmax = 34.2992083765300
vlimit exceeded for step 454 ; vmax = 20.4352793225986
vlimit exceeded for step 455 ; vmax = 25.8498620648548
vlimit exceeded for step 456 ; vmax = 20.3609995780702
..
..
..
-----------------------------
When I check out the trajectory file (when ntwx=1 to see it better), I see
that at some time, the methane molecule starts to move fast and the whole
system blows up.
Then, I set the dt=0.001 and run the same simulation. Now, I dont get any
vlimit problem, and the trajectory file gives a nice/smooth movie in VMD.
My question is, why does this dt=0.002 blow up my system? Thanks in
advance.
Best,
--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Sat Feb 26 2005 - 01:53:00 PST
