Re: [AMBER] sudden and rapid configuration change in NVT simulation

From: yjlee <>
Date: Fri, 06 Jun 2014 21:46:03 +0900

Dear Jason, and Amber users.


Thank you again for pointing that. I'll try with cutoff value larger
than 8 A


I think I'm using polarizable force field, ff02 force field.
To say exactly, I excuted xleap with (leaprc.ff02polEP.r1) file and
saved the prmtop and inpcrd file with (saveAmberParmPol) command.

I thought (ipol = 1) should be mentioned in input file, since I read
(Use saveAmberParmPol to save the prmtop file, and set ipol=1 in the
sander input file) from the AmberTools12 manual...

I'm using Amber11. What is the "current version" that you mentioned?


The polarizable force field might be the answer for this problem.

Today I did same simulation, but using TIP3P model with ff99SB force
Since it is not polarizable, I wrote (ipol = 0) in input file.
Actually this was the only difference in input file.


But still I don't get it.
Is there a problem applying the polarizable force field? or POL3 water

* The reason that I'm using polarizable force field is, I want to use
POL3 water model (which is polarizable) in my simulation.

* I installed AmberTools14, to use CPPTRAJ program with (autoimage)
Still, however, I'm using Amber11 and old version of Ambertools for MD


Any suggestion or comments would be very appreciated.

With many thanks in advance,


>> cut = 6.0,
> This cutoff is way too short. You should be using at least 8 A.
>> ipol = 1,
> Are you _sure_ that you are using a polarizable water model? Even if
> you
> are, the current versions of Amber set the ipol flag in the topology
> file.
> You should get rid of this variable from your input file.
> In general, you can't just "turn on" polarizability for any force
> field.
> You must select a polarizable force field.

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Received on Fri Jun 06 2014 - 06:30:03 PDT
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