[gmx-users] Regarding POPE " H " atom type modification

[naga raju]

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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