[gmx-users] rvdw and rcoulomb

[Justin Lemkul]

On 3/13/18 7:23 AM, Ahmed Mashaly wrote:
> 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?

With PME, the value of rcoulomb becomes somewhat irrelevant, but in 
general, one should *not* deviate from prescribed force field cutoff 
values. Force fields are parametrized under a certain set of 
assumptions. If you then deviate from those assumptions, you potentially 
imbalance forces. The simulation will happily run and potentially 
produce incorrect results.

Find the proper values in primary literature (something everyone should 
do before even deciding on a force field) and use those values. GROMACS 
will tune rcoulomb slightly for PME performance reasons, and this is 
fine, but don't go messing with the stock values haphazardly.

-Justin

> 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
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> 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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-- 
==================================================

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

==================================================