[gmx-users] Re: gmx-users Digest, Vol 114, Issue 15

Hari Pandey harichem12 at yahoo.com
Mon Oct 28 20:04:03 CET 2013

Dear Gromacs Users,

First, I would like to thank Dr. Lemkul for reply.

My problem description is as follows:
I am using CHARMM36  forcefield to equilibrate of AOT. when I add the mass of all atoms from topology, it gives me 444.5 which is correct but when I run the script

editconf -c  -f A.gro -o A.gro   -density 1000  -bt cubic -box  5 -d 0.1 .

It  display incorrect value for mass of input.  The mass of input should be 444.5 . The out come of above script is:

Volume: 125 nm^3, corresponds to roughly 56200 electrons
No velocities found
    system size :  0.215  0.234  0.157 (nm)
    diameter    :  0.287               (nm)
    center      :  2.500  2.500  2.500 (nm)
    box vectors :  5.000  5.000  5.000 (nm)
    box angles  :  90.00  90.00  90.00 (degrees)
    box volume  : 125.00               (nm^3)

WARNING: masses and atomic (Van der Waals) radii will be determined
         based on residue and atom names. These numbers can deviate
         from the correct mass and radius of the atom type.

Volume  of input 125 (nm^3)
Mass    of input 967.25 (a.m.u.)
Density of input 12.8493 (g/l)
Scaling all box vectors by 0.234221
new system size :  0.050  0.055  0.037
    shift       :  1.914  1.914  1.914 (nm)
new center      :  2.500  2.500  2.500 (nm)
new box vectors :  5.000  5.000  5.000 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 125.00(nm^3)
Here we can see that mass of input is  967.25 which is far beyond the reality. this will cause error in density and all other mass dependent parameters. 

Please  help me how do I come over to this error
Thank you so much for you kind help


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