[gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 93
wangtaoone at hotmail.com
Wed May 25 15:22:41 CEST 2016
You have mentioned that i missed my itp file.Here is it
[ moleculetype ]
[ atoms ]
;id at type res nr residue name at name cg nr charge mass
1 opls_434 1 OHIN OH 1 -1.300 15.999
2 opls_435 1 OHIN HO 2 0.300 1.008
[ bonds ]
;i j funct length force.c
1 2 1 0.09450 462750.4;
As you can see, that is how i defined the itp file of OH-.
Those parameters can be found in oplsaa.ff/ffbonded.itp and oplsaa.ff/ffnonbonded.itp files.They have been provided in gromacs version 4.6.7.
Here are they:
HO OH 1 0.09450 462750.4 ; SUG(OL) wlj mod 0.96-> 0.945
opls_434 OH 8 15.99940 -1.300 A 3.20000e-01 1.04600e+00
opls_435 HO 1 1.00800 0.300 A 0.00000e+00 0.00000e+00
But i really don't understand why the bond in OH- is invalid.Or in another word,what can i do to finish an sucessful energy minimization with OH- in my system?
You also said that waht i am conduncting is not a true constant PH MD.Yes,you are right.I did have some misunderstanding about it. But in my system ,i intended to create an environment where there is plenty of OH-with fixed concentration of it.So fixed protonation is ok in this work. But anyway, i am very interested in constant-PH MD,and want to do something about it.I would spend more time on it.
Now,would you please offer me some advice on solve my problem above?
Date: Wed, 25 May 2016 07:04:59 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] gromacs energy minimization fatal error:
Invalid bond type 1000 in constant-PH MD
Message-ID: <fe760a05-25f0-7190-0003-139be796e0ee at vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 5/25/16 6:06 AM, Wang Tao wrote:
> Hi,every one!
> I'm using opls aa in gromacs to conduct constant-PH MD. In my system,PH is equal to 13.There are three kind of groups, NA+,OH- and H2O. The itp file for OH- is created by myself.
This is not what constant pH MD is. You've got a fixed protonation state with
OH- floating around, which may not be physically realistic.
> After having finished the genbox and genion steps sucessfully, i met a problem in energy minimization step. The output information says:Invalid bond type 1000. But i don't really understand what the exact problem is.
> Tried to remove bond definition in itp file for OH-, don't work.
> Tried to remove bond definition in ffbonded.itp for OH-, don't work.
> Replaced OH- with CL-,error infomation disappeared.
> I believe the problem is related to OH- force field parameters,but don't know how to deal with it.
You haven't provided us with its topology, so there's nothing anyone can do but
guess haphazardly. But if removing it solves the problem, you know exactly
where the issue is.
> Can anyone help me?
> Tao Wang
> Thank You!
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
More information about the gromacs.org_gmx-users