I have seen a similar problem with my softcore simulations.
I can't tell you what the "developer answer" is to this
question, but here is what works for me: use a very small
time step for NPT (constant pressure equilibration) simulations.
I have used around 0.0001-0.0005 for success. Then I use NVT
(constant volume) with larger time steps for production simulations.
Like I said, I'm not sure what the problem is, so I can't tell
you the root cause. My ligands are around 55 atoms with
3 positive charges. Large ligands with charges may be
problematic.
Hope this helps ...
--Niel
________________________________________
From: anyiphysics.gmail.com [anyiphysics.gmail.com]
Sent: Monday, April 18, 2011 1:05 PM
To: amber.ambermd.org
Subject: [AMBER] 'shake problem' and soft core potential
Hi all,
I tried to calculate delta G binding between two ligands using soft core
potential. I was able to finish energy minimization for all steps but when
I did equilibration for step2 (the one with soft core turned on) I
encounter such a problem:
'vlimit exceeded for step 1759; vmax = 30.3383
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 360 720 721
Note: This is usually a symptom of some deeper
problem with the energetics of the system.'
I checked my coordinates and trajectories and found no close contact or
atom overlap in the coordinates.
My input file is:
' &cntrl
imin = 0, ntx = 1, irest = 0,
ntf = 1, ntc = 2,
ntb = 2, cut = 12.0,
nstlim = 50000, dt = 0.002,
temp0 = 300.0, ntt = 3, gamma_ln = 5,
ntp = 1, pres0 = 1.0, taup = 0.2,
ntpr = 1000, ntwx = 1000, ntwr = 5000,
icfe=1, clambda = 0.1,
ifsc=1,
crgmask=':1.N1,C6,H6,C5,C7,H71,H72,H73,C4,O4,N3,H3,C2,O2',
scmask=':1.N1,C6,H6,C5,C7,H71,H72,H73,C4,O4,N3,H3,C2,O2',
&end'
I set ntf =1 since it is required. I also did a heating up without density
equilibration separately. However, same problem occurred again.
I would like to hear your comments and advice on my problem. Thank you very
much.
Yi An
Graduate student
Department of Chemistry
Texas A&M University
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Received on Mon Apr 18 2011 - 14:30:02 PDT
