[gmx-users] Flat-bottomed position restraint set

[liuyong_1007 at dicp.ac.cn]

Dear Erik,

Thanks for your reply! I use a larger cut-off of the non-bonded interaction. But water molecules sitll escape to the vacuum after a 220 ns MD run. 
The restraints are applied to the O atoms.  Could you please help me to check whether the sets of the equil.mdp and topol.top files are right or wrong? 
The files are shown in the attachment. Thank you very much !

Best regards,
Yong Liu

liuyong_1007 at dicp.ac.cn

From: Erik Marklund
Date: 2014-11-14 19:24
To: <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Flat-bottomed position restraint set
Dear Liuyoung,

Remember that the electrostatic screening is much weaker in gas phase systems such as yours. I would use a larger cut-off for the non-bonded interactions to effectively have all vs all interactions. Your system is fairly small so you won't be simulating for that long anyway. Note that gromacs can be told to keep the neighbour list from the first frame, which would speed up things a bit.

Kind regards,
Erik


Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

On 14 Nov 2014, at 07:15, liuyong_1007 at dicp.ac.cn<mailto:liuyong_1007 at dicp.ac.cn> wrote:

Hi Justin!
I try to apply restraint just to the O atom. There is another question about  the set of the coulomb and the vdw interaction for the ion-water cluster Na(H2O)_250. My set is shown as follow:

; vdw
vdw-type      = Cut-off
rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = cut-off ;Reaction-Field ;Generalized-Reaction-Field ;cut-off ^M
rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)^M
epsilon_rf      = 2.0
epsilon_r       = 0.5
cutoff-scheme    = group

The radius of the cluster is about 1.12 nm. Is this set appropriate ?

Best regards,
Yong Liu



liuyong_1007 at dicp.ac.cn<mailto:liuyong_1007 at dicp.ac.cn>

From: Justin Lemkul
Date: 2014-11-14 10:40
To: gmx-users
Subject: Re: [gmx-users] Flat-bottomed position restraint set


On 11/13/14 7:15 PM, liuyong_1007 at dicp.ac.cn wrote:
Hi Justin!
I use the geometric center of the sphere as the reference coordinates. However, there are still water molecules escaping to the vacuum. Is there other way to aovid this ?


This shouldn't happen if things are set up right.  Try applying the restraint
just to the O atom, not all 3 atoms of the water individually.  We do this
routinely and it works quite well.

-Justin

Best regards,
Yong Liu



liuyong_1007 at dicp.ac.cn

From: Justin Lemkul
Date: 2014-11-12 21:54
To: gmx-users
Subject: Re: [gmx-users] Flat-bottomed position restraint set


On 11/12/14 8:08 AM, liuyong_1007 at dicp.ac.cn wrote:
Dear Gromacs users!

I use the flat-bottomed position restraints to avoid the molecules to escape from the clusters to the vacuum. The parameters of the restraints on water molecules are shown as follow:
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i   funct       g         r(nm)       k
    1    2        1          3         30.0
    2    2        1          3         30.0
    3    2        1          3         30.0
#endif
However, water molecules still escape away from the cluster to the vacuum after about 100 ns MD run at 550K. What should be done with the restraints to avoid the water molecules to escape to the vacuum?


Are you using suitable reference coordinates passed to grompp -r?  If you're
not, then the reference coordinates are whatever is in grompp -c, which means
your water molecules can deviate up to 3 nm from that position without penalty.
  For a sphere, the reference coordinates for the water should be the geometric
center of the sphere.

-Justin


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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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