[gmx-users] Re: FEP + Ham. REMD

[Yuri Garmay]

Have anybody been constructing virtual sites for calculating PMF via FEP?


2013/4/6 Yuri Garmay <yuri.from.spb at gmail.com>

> Hi all!
>
> I have a problem. So as it can be seen in the theme I am trying to improve
> sampling of free energy calculating simulation by using replica exchange.
> In the gmx4.6 it is simple while using FEP technique, but does not
> implemented for umbrella sampling. But I want evaluate potential of mean
> force between two flexible molecules, so I have decided to do this with
> FEP+REMD.
>
> It is desirable to select distance between the mass centres as a reaction
> coordinate, but FEP has to do with bonds or constraints between single
> atoms. Luckily there virtual sites are possible to define in gromacs. So I
> have a thought of using it.
>
> But I have never been using virtual sites and so have some questions.
> I  introduced two virtual sites in topology with these lines:
>
> --------------------
> *.top:
> [ atomtypes ]
> ;name mass charge ptype sigma epsilon
> DD 0.0 0.0 V 0 0 ; nb interaction off?
>
> [ implicit_genborn_params ]
> ; Atomtype sar st pi gbr hct
> DD 0.0 0 0.0 0.0 0.0 ; interaction with solvent off?
>
> [ atoms ]
> .......some lines .....
>    111         DD      9    DDD     DD    111          0
>    112         DD     10    DDD     DD    112          0
>
> [ virtual_sitesn ]
> ; Site from funct a d
> 111    2       1    2 ... ; virtual site at mass centre of some groupe
> 112    2       82   83 ...
>
> [ bonds ]
> ....
>   111   112     6           0.3           1000            1.3
> 1000 ; harmonic bond
> ....
>
> *.gro:
>     9DDD     DD  111   0.000   0.000   0.000 /// position have to be
> determined automatically?
>    10DDD     DD  112   0.000   0.000   0.000
> ------------------
>
> The energy minimization showed correct constraint length at first sight.
> But does this method solve problem I have? I will be very much appreciated
> if someone experienced explains me whether this is correct or there are
> pitfalls at this way.
>
>
> --
> Best regards,
> Yuri
>
>


-- 
Best regards,
Yuri