What if you generate a pdb and look at it?
My first guess is that reordered atoms is the issue, if you are using
the rst from another topology.
Bill
On 6/2/16 1:37 PM, Morteza Chehel Amirani wrote:
> 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 - 15:30:02 PDT
