Hi
I replaced one of water molecules (kept the rest) with H2O2, and made a new
topology file (using the very initial box sizes). Then, I resubmitted a new
minimization task, but got the following error. I did not get such an error
when removed all water molecules and made a new solution box. So, my guess
is that the problem is due to inconsistency in the water box and initial
box sizes.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++
NSTEP ENERGY RMS GMAX NAME NUMBER
1 3.1809E+26 3.9876E+26 1.3031E+29 O 101322
BOND = 955.4185 ANGLE = 2381.6195 DIHED =
4076.9076
VDWAALS = ************* EEL = -295055.5049 HBOND =
0.0000
1-4 VDW = 1145.9917 1-4 EEL = 8556.4582 RESTRAINT =
0.0000
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
31 6.8661E+21 2.9243E+20 2.6835E+22 O 71409
BOND = 959.5732 ANGLE = 2381.5994 DIHED =
4076.8960
VDWAALS = ************* EEL = -383500.4777 HBOND =
0.0000
1-4 VDW = 1146.0149 1-4 EEL = 8556.3762 RESTRAINT =
0.0000
***** REPEATED LINMIN FAILURE *****
+++++++++++++++++++++++++++++++++++++++++++++++++++++++
Also, using the rst file of that minimization (I did not notice the error
of the minimization at that point, so likely used a restart file which was
already failed!), I submitted a dynamic simulation, but got the following
error (which is absolutely possible!):
+++++++++++++++++++++++++++++++++++++++++++++++++++++++
vlimit exceeded for step 0; vmax = **********
Coordinate resetting cannot be accomplished,
deviation is too large
iter_cnt, my_bond_idx, i and j are : 1 2 138 140
+++++++++++++++++++++++++++++++++++++++++++++++++++++++
I'm wondering if there is any thoughts on this?
Sincerely,
Morteza
On Thu, May 26, 2016 at 4:21 PM, Morteza Chehel Amirani <
morteza.amirani.gmail.com> wrote:
> Hi
>
> I have a simulation which was running for 10 ns. Now, I want to replace
> one of water molecules with a hydrogen peroxidase. I'm wondering what the
> best way is to kind of restart the simulation?
> Do I need to prepare the topology file from the scratch, or I can make a
> new topology file only for the peroxide and combine it with the original
> one?
>
> In the case I make the a new topology file for the new system, how can I
> import the simulation box information into it?
>
> Sincerely,
> Morteza
>
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Received on Thu Jun 02 2016 - 14:00:02 PDT
