Deleting one molecule per each frame is rather easy task to do in Amber (in
cpptraj). Then, only to carefully program input generation, or more
precisely a loop from one to XX deleted molecules. I have two types of
solvents, in which one is evaporating, whereas the second one forms
something like a solid phase (as observed experimentally)... Lots of files
are generated indeed.
I think that periodicity shouldn`t be such an issue as I have new topology
files after each deleting (original minus number of deleted molecules). With
no periodicity (no constant volume nor pressure), the system wouldn`t have
to be stable (could spread out or slowly starting exploding).
The question now is how could I simulate evaporation in external electric
field? (as the field cannot be used with NPT, and I need NPT to adjust
density after deleting successively)
Michal
"
Message: 2
Date: Tue, 30 May 2017 14:46:57 -0700
From: Bill Ross <ross.cgl.ucsf.edu>
Subject: Re: [AMBER] external electric field in Amber 16
To: amber.ambermd.org
Message-ID: <5887b5f0-500c-a33f-8ff8-5695bb7f9f1e.cgl.ucsf.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
Deleting molecules in succession is likely to be a labor-intensive
exercise in Amber, plus which, if there is evaporation shouldn't there
be a surface and no periodicity? If you get into deleting successively,
you will likely want to script or program input file generation, since
there would be a lot of it, if not make major changes to the source
code, which might be necessary to in any case.
Bill
On 5/30/17 2:06 PM, michal biler wrote:
> I see. Setting ntb = 1 should keep constant V. Anyway, this is still the
> case with no pressure scaling: ntp = 0 (as external electric field cannot
be
> apperantly used when npt 0). What if I need to delete one molecule per
each
> frame (to simulate evaporation), therefore pressure has to be taken into
> account and has to be equilibrated while using the electric field? How
> should I proceed?
>
> "
> Message: 19
> Date: Tue, 30 May 2017 10:43:23 -0400
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Subject: Re: [AMBER] external electric field in Amber 16
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAGk3s-SPHyLEkYe4R+3U8Ua09USS8f1EsdxdOUGMgpKWa4PUFQ.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> your system shouldn't explode at constant volume. are you sure you have
ntb
> set right? If it is unstable at constant V, make sure you equilibrate a
> while at constant P, then switch to constant V.
>
> On Tue, May 30, 2017 at 10:39 AM, michal biler <michal.biler.seznam.cz>
> wrote:
>
>> Dear Amber users,
>>
>> I want to use an external electric field in Amber 16. After specifying
efz
>> values, I got this error message:
>>
>> | ERROR: External electric fields cannot be used when npt > 0!
>>
>> If I turn off the pressure scalling (ntp = 0), the simulation runs, but
of
>> course, the system is kind of exploding as I do not have any pressure.
>>
>> I found a link to the similar question (http://archive.ambermd.org/
201705/
>> 0126.html) ...anyway, is there a way how to do such simulations with both
>> external electric field and pressure on? I think, long simulations would
>> not
>> make a sense without ntp.
>>
>> Thank you!
>>
>> Michal
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
"
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Received on Wed May 31 2017 - 14:30:02 PDT
