> 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)
How about a 2-stage equilibration at each step: first density, then with the field?
I didn't follow discussion of why the field can't be used with NPT; if it is the science, then you may be stuck, else some programming would be in order.
Bill
On 5/31/17 2:22 PM, michal biler wrote:
>
> 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
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
> "
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 31 2017 - 17:30:02 PDT
