Re: [AMBER] Simulation does not restart from restart file written in previous step.

From: Abhilash J <>
Date: Fri, 4 May 2018 17:49:38 +0530


   I changed iwrap=1 to 0, but after some time the following error
occurred. I think it is due to iwrap being now 0.
   Now situation becomes i cannot either use iwarp=1 or iwrap=0.
   Only possible solution seems to be changing to NetCDF restart file
format. Which i will try as see if it helps the situation here.
   So I just wanted to discuss whether (in general) iwarp should be kept as
0 or 1 (David suggested that iwrap should always be kept to 0)
   And is there any other solution to this problem.

| ERROR: I could not understand line 47786
  32.8057711 149.6906285************ 32.5235640 150.5729558************

*s in the inpcrd file often indicate an overflow of the Fortran format used
to store coordinates in the inpcrd/restart files. This often happens when
coordinates are not wrapped into the center cell (when iwrap = 0) and some
particles diffuse too far away. Try restarting from your last good restart
file and setting iwrap=1 or using a NetCDF restart file format. See the
Amber manual for details

On Thu, Mar 8, 2018 at 6:01 PM, Abhilash J <> wrote:

> Hi,
> I did use iwrap=1 in this simulation.
> After having a look at the structure of complex with water at end of
> the last frame of the simulated trajectory, iwrap=1 does look as the most
> probable cause.
> Regards
> On Wed, Mar 7, 2018 at 7:22 PM, David A Case <>
> wrote:
>> On Wed, Mar 07, 2018, Abhilash J wrote:
>> >
>> > Thanks, Ruchika and Case for the help.
>> > Last restart file showed ligand far from the protein cavity.
>> > making a new restart file using autoimage command solved the issue.
>> Not sure if this is relevant or not: you should not use iwrap=1 in
>> simulations like this, since it may have been wrapping that caused the
>> symptoms you reported. [Of course, ignore this if you were not using
>> wrapping.]
>> (Regular readers of this list know that I think there are no types of
>> simulation where iwrap=1 is appropriate.)
>> ....dac
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Received on Fri May 04 2018 - 05:30:06 PDT
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