[gmx-users] free energy perturbation

[Mikhail Mazo]

Dear Gromacs-users and developers,
 
I use GROMACS for studying the hydrotation free energy of alkane
molecules 
using the free energy perturbation method. Thereto I calculated
trajectory 
and energy for l=l0 (as an example for l=0.8) 
and energy for l=0.6, l=0.4, l=0.2 using programs:
 

mdrun -s Eth_for_md.tpr -o Eth_08_traject.trr -c Eth_after_08md.gro -v
-e Eth_08_energy.edr 

 

mdrun -rerun Eth_08_traject.trr -s Eth_for_md.tpr -c Eth_after_08md.gro
-v -e 

 
However, the values "Coulomb-14", "Coulomb (SR)" and "Coulomb (LR)" for
all l*0.8 were the same (and differed from the values for l=0.8).
Furthermore, the values "Box-X, "Box-Y" and "Box-Z" for the cases l*0.8
increased.
 
What does it mean?
 

Topology file of C2Н6 was:

 

[ moleculetype ]

Eth      3

 [ atoms ]

 ;  nr  type resnr resid  atom  cgnr   charge    mass      typeB
chargeB   massB

     1  opls_135 1  C2     C1      1   -0.180    12.011     opls_135
0.000    12.011

     2  opls_140 1  C2     H11    1    0.060      1.008     opls_140
0.000      1.008

     3  opls_140 1  C2     H12    1    0.060      1.008     opls_140
0.000      1.008

     4  opls_140 1  C2     H13    1    0.060      1.008     opls_140
0.000      1.008

     5  opls_135 1  C2     C2      1   -0.180    12.011     opls_135
0.000     2.011

     6  opls_140 1  C2     H21    1    0.060      1.008     opls_140
0.000      1.008

     7  opls_140 1  C2     H22    1    0.060      1.008     opls_140
0.000      1.008

     8  opls_140 1  C2     H23    1    0.060      1.008     opls_140
0.000      1.008

 [ bonds ]

   1   2

::::::::::::::::::::

:::::::::::::::::::::

 
And the second question. 
There are two unintelligible strings in the heading of file runavgdf.xvg
(result of the program g_energy with option -f2):
 

@ view 0.15, 0.15, 0.75, 0.85 

@ legend 0.78, 0.8 
 
What does its mean?

 

 
Thank you in advance,
 
Mikhail Mazo
 
Dr. M. Mazo
Computer Simulation Group

Department of polymers and composites

Institute of Chemical Physics 
Kosygina 4, Moscow
119991, Russia 
Tel.: 07 (095) 939-7515
e-mail: mikhail.mazo at algodign.com 
 

 

 

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