Dear gmx users,
I am trying to equilibrate POPE lipid
bilayer. As per mailing list
(http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html.),
C6/C12 parameters are converted into sigma/epsilon. I
modified " H " atom type to opls_369 in pope.itp
file(show below).
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[ atoms ]
; nr type resnr residu atom cgnr
charge mass
1 opls_369 1 POPE H1 0
0.4000 1.0080 ; qtot:0.36
2 opls_369 1 POPE H2 0
0.4000 1.0080 ; qtot:0.72
3 opls_369 1 POPE H3 0
0.4000 1.0008 ; qtot:1.08
4 LNL 1 POPE N4 0
-0.5000 14.0067 ; qtot:0.76
5 LH2 1 POPE C5 0
0.3000 14.0270 ; qtot:1.0
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I didn't get any error messages while runing "grompp"
command.
But when runing mdrun commnad, i got the fallowing
error.
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Step 33, time 0.066 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.037791 (between atoms 6057 and 6105) rms
0.000470
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint
length
6057 6105 90.0 0.1000 0.1038 0.1000
Step 34, time 0.068 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.001669 (between atoms 6057 and 6105) rms
0.000025
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint
length
6057 6105 58.4 0.1038 0.1002 0.1000
Step 35, time 0.07 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.005961 (between atoms 6057 and 6105) rms
0.000082
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint
length
6057 6105 68.1 0.1002 0.0994 0.1000
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My question is
1) Where I have to modify H atom type
given in pope.itp file ( given that "added atomtype H
from opls_369 to match H expected by pope.itp" in
atomtypes section:
http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html.)
Any suggestion is appreciated.
Thank you in advance
with best regards,
Nagaraju
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