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 <jalem...@vt.edu>
To: gmx-us...@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.szil...@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 <jalem...@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

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

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


--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.


--
==================================================

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

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

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

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

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Reply via email to