[gmx-users] Flat-bottomed position restraint set

liuyong_1007 at dicp.ac.cn liuyong_1007 at dicp.ac.cn
Fri Nov 14 08:15:32 CET 2014

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

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.


> 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

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