[gmx-users] rvdw and rcoulomb

[Ahmed Mashaly]

Dear Justin,

What do you mean by incorrect?
I understand it is higher than it should be (0.8 - 1 nm), it will consume more time, but won't give wrong results, am I correct? 
Kind Regards,
Ahmed 

________________________________
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org 
Sent: Tuesday, March 13, 2018 12:18 PM
Subject: Re: [gmx-users] rvdw and rcoulomb





On 3/13/18 5:17 AM, Ahmed Mashaly wrote:
> Thanks guys
>
> It is AMBER ff
> Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 for continuation with no effect on the results? And if I do the other restarts starting from 1 or it will give different results?

You shouldn't switch physical models mid-simulation. Start over using 
the correct value (1.2 nm is incorrect for AMBER, anyway).

-Justin

> On Mon, 12 Mar, 2018 at 4:37 pm, Szilárd Páll
>> <pall.szilard at gmail.com> wrote:
>> Note that rcoulomb, unlike rvdw, when using a PME long-range
>> electrostatics, is tunable (together with the PME grid spacing).
>> --
>> Szilárd
>>
>>
>> On Mon, Mar 12, 2018 at 3:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>> On 3/11/18 7:33 PM, Ahmed Mashaly wrote:
>>>> Dear users,
>>>> Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind
>>>> Regards,Ahmed
>>>>
>>> These values are a function of the force field and are not freely tunable.
>>>
>>> -Justin
>>>
>>> --
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>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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