[gmx-users] free energy calculations for reference state for constant pH MD simulations...

[Justin Lemkul]

On 1/30/14, 2:27 PM, Ozbil, Mehmet wrote:
> For Dummy atom, I tried to write DUM for atom type and give 0 charge but it could not recognize the atom type. Then I just wrote the atom type with 0 charge but as I understand I could not make it a dummy atom. How can I do it?
>

The DUM type has no parameters assigned in ffnonbonded.itp in oplsaa.ff for some 
reason.  You can easily add it; it has zero mass, zero charge, and zeroes for 
sigma and epsilon.

> And also for the parameters, I understand the fact that the bonding and non-bonding interactions will change, but I could not find  a good example or I could not understand how to do it? In the manual, Section 5.7.4 there is an example but I don`t understand where the gb_ parameters are coming from:
>

Unfortunately, the example is for Gromos96, which happens to work differently 
from all of the other force fields in Gromacs.  The gb_*, ga_*, etc are simply 
macros for copying and pasting parameters from ffbonded.itp.  The general form 
of the topology is always observed; see Table 5.5.

> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
> 1 H 1 PROP PH 1 0.398 1.008 CH3 0.0 15.035
> 2 OA 1 PROP PO 1 -0.548 15.9994 CH2 0.0 14.027
> 3 CH2 1 PROP PC1 1 0.150 14.027 CH2 0.0 14.027
> 4 CH2 1 PROP PC2 2 0.000 14.027
> 5 CH3 1 PROP PC3 2 0.000 15.035
> [ bonds ]
> ; ai aj funct par_A par_B
> 1 2 2 gb_1 gb_26
> 5.7. File formats 135
> 2 3 2 gb_17 gb_26
> 3 4 2 gb_26 gb_26
> 4 5 2 gb_26
> [ pairs ]
> ; ai aj funct
> 1 4 1
> 2 5 1
> [ angles ]
> ; ai aj ak funct par_A par_B
> 1 2 3 2 ga_11 ga_14
> 2 3 4 2 ga_14 ga_14
> 3 4 5 2 ga_14 ga_14
> [ dihedrals ]
> ; ai aj ak al funct par_A par_B
> 1 2 3 4 1 gd_12 gd_17
> 2 3 4 5 1 gd_17 gd_17
>
> Also here the example for Gromos forcefield but I am using OPLS force field so I assume these numbers will be different as well. How can I find the parameters for B state for OPLS force field?
>

All of that information is in ffbonded.itp, as it is for all force fields.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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