Thanks Niel,
I think this problem has been solved with your suggestion. Also I found
that I need to use a large gamma_ln value to make sure the temperature is
around 300K. I think with proper time step and thermostat, you could also
heat the system from 0 to 300K before density equilibration.
Yi
On Apr 18, 2011 4:19pm, Niel Henriksen <niel.henriksen.utah.edu> wrote:
> 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 Fri Apr 22 2011 - 14:00:04 PDT
