[gmx-users] How to scale epsilon parameters of Lennard-Jones term in .top file?

Jianguo Li ljggmx at yahoo.com.sg
Mon Dec 8 08:12:29 CET 2014

To run REST in gmx using lamda-dynamics, you need to edit both ffnonbonded.itp and ffbonded.itp. 
In ffnonbonded.itp, you need to define a new atom type corresponding to state B, you need to add something like:; name             bond_type       mass          charge   ptype          sigma      epsilon 
opls_001_ B      C             6     12.01100     0.500       A    3.75000e-01  2.19660e-01 ...The charges for state_B can be added in the topology file.For bonded parameters you need to rescale the force constants in all sections of ffbonded.itp.Finally you also need to edit ions.itp to make sure that the total charges for state_B is zero.

     On Monday, 8 December 2014, 9:14, 周双艳 <zhoushy13 at lzu.edu.cn> wrote:

 Hi all,
I am trying to run REST in GROMACS following the way proposed by tsuyoshi terakawa. In their method,they implemented REST by rescaling the force-field parameters without even changing the code. I have also searched in the mailing list and found that we can manipulate the scale parameter in ffnonbonded.itp and ffbonded.itp as well as the .rtp file for charges to construct the .top of highest "temperature" which corresponds to lambda=1.Taking the two states(the lowest "temperature" corresponds to lambda=0 regard as state A and highest temperature corresponds to lambda=1 regard as state B) into the same .top file, and then we can directly use the Hamiltonian REM routine of GROMACS 4,which is based on the λ-dynamics and the linear combination potential scheme of the two-ends potentials(I do not know whether my understanding is right?).
I add the parameters of state B in to the topology A following the 5.7.4 "Topologies for free energy calculations" in GROMACS manual.The bond scaling parameters can be added in [bonds] with dA kA dB,kB,where the dA,kA,stand for the bond parameters of state A,and the dB,kB stand for the parameters of state B.Other scaling parameters such as [angles],[dihedrals] can be treated as the same way.My question is how to add the epsilon parameters of Lennard-Jones of state B into the .top file? The force field that I used is OPLS-AA force field,is it true to add the epsilon value in the [pairs] part? I do not know in [pairs] with the format of :ai aj funct c0 c1 c2 c3,what c0,c1,c2 and c3 stands for? 
Would you some body give me some suggestions? thanks very much
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