Hello all,
An update regarding the previous issue. I have gone through the previous
answers on the mailing list regarding the similar error. I have tried to
trace out the error but I wasn't successful. I would also like to point out
that I checked for clashes at the point where dynamics stopped, but there
doesn't seem to be any active clashes. Here I am adding more details about
my system and the methodologies followed. Kindly spare some time to go
through the mail
My protein system contains an iron(iii) coordination centre at the active
site with hydroxyl group as one of the ligands. Earlier I have performed
dynamics with Fe(IV)-oxo system where the dynamics worked fine. I took one
of the pdbs from trajectories of Fe(IV)-oxo system, added hydrogen to the
oxygen and prepared Fe(III)-hydroxyl system input files using MCPB.py
program. The parameters were calculated from QM calculations utilizing
Gaussian 09 software.
I have tried to perform energy minimization with usual parameters
(including SHAKE, restriction of 20 Kj mol-1 A -1 at the active site ), but
the minimization failed. Whereas the minimization without SHAKE restraint
(including restraint of 20) worked fine. Thereafter, I tried to carry out
heating with the NVT conditions with restraint of 20, followed by NTP
equilibration for 1ns. It worked just fine till this point, but when I try
to restart the simulation with a lesser restraint, the dynamics gave the
error that was reported in earlier mail. To resolve the energetics, I have
even tried relaxing of restraint at the active site in 5 steps. Firstly
energy minimization with a restraint of 8, followed by equilibration for
50ps with a restraint of 8. Second step included energy minimisation with a
restraint of 6 followed by equilibration for 50ps with a restraint of 6.
The same cycles were repeated until the restraint reached 0. But again when
I run longer runs after this point, the dynamics failed with the same error.
Even the production run under NVT conditions failed with similar error.
I have tried to check the atom numbers and found that 4822 and 4823
correspond to the oxygen and hydrogen atoms of OH group that is bound to
Fe(III) at the active site. I am trying to understand where the problem
lies. Could it be the wrong parameters that's causing trouble ? It would be
really helpful is some one provides some insights on this.
Any help would be much appreciated.
Thank you for your time
Asmita
On Thu, Mar 1, 2018 at 7:01 PM, ASMITA SEN <senasmita1.gmail.com> wrote:
> Hello,
>
> I am trying to do classical MD simulation with a Fe(III)-OH metalloenzyme
> system having 40000 atoms (including water molecule) . I run minimisation
> with 5000 steepest descent and 10000 conjugate gradient steps restrainning
> the active site with a restraint value of 20 kcal mol-1 A-2 .The system
> then gently annealed from 0 to 300 K for 50 ps with the same constraint
> followed by a 1ns of density equilibration under an NTP ensemble at a
> target temperature of 300 K and a target pressure of 1.0 atm using ntt=3
> and Berendsen barostat with a collision frequency of 2ps with a restraint
> of 10 kcal mol-1 A-2. Thereafter I reduced the restraint weight in 5
> steps i.e with a restraint of 8, 6, 4, 2, 0. But I find some errors like
> "vlimit exceeded for step" . The error message is as follows,
>
> vlimit exceeded for step 5804; vmax = 32.7330
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 2333 4822 4823
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
> Can you please tell me how do I solve this type of problem?
>
> --
> Asmita Sen
> C/o- Dr. Gopalan Rajaraman
> Junior Research Fellow (CSIR)
> Department of Chemistry
> IIT Bombay, Powai,
> Mumbai- 400076, India
>
--
Asmita Sen
C/o- Dr. Gopalan Rajaraman
Junior Research Fellow (CSIR)
Department of Chemistry
IIT Bombay, Powai,
Mumbai- 400076, India
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Received on Fri Mar 09 2018 - 12:30:02 PST
