>zhangjianguo2002 wrote:
>>  
>>  
>>    Firstly, thanks Berk and David van der Spoel for your replies. Maybe 
>> I have not explain my problems clearly, there is only one type of 
>> particle,namely one full-atom benzene molecule is replaced by one 
>> coarse-grained benzene particle,so there in no non-bonded interactions 
>> between different types and comb-rule may not work.
>> in the [ defaults ] section of the ITP file, the defaults power for the 
>> repulsion term is 12, if I change it to 9, is that enough  if I want to 
>> use LJ-9-6 potential? is there still anything needed to be changed?
>>  
>That is not enough. Please read carefully our previous answers.
 
Thanks very much for your suggestions! I just want to use LJ-9-6 potential by 
providing sigma and epsilon parameters, that would be easer to change the 
potential by changing sigma and epsilon values than by changing potential 
table, does GROMACS support this ? or does GROMACS only support potential 
tables if the power of the repulsion term is not 12 ?
 

>
>> Best regards!
>> 
>> 
>>     >Hi,
>>     >
>>     >I forgot about this feature.
>>     >Your problem is indeed that you used comb-rule=1,
>>     >you have to use 2 or 3 to make this work.
>>     >And indeed you should use user tables filled with the 9-6 potential.
>>     >
>>     >Gromacs could actually easily support p-6 tables with any value for p,
>>     >by storing p in the tpr file and automatically using tables when p!=12.
>>     >
 
Thanks for your reply, do you mean that if p !=12 ,I have to change p to the 
value I want ,at the same time I have to provide a potential table according to 
LJ-P-6?
 
 

>>     >Berk
>>     >
>>     >> Date: Tue, 26 May 2009 09:45:22 +0200
>>     >> From: sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
>>     >> To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
>>     >> Subject: Re: [gmx-users] Lennard-Jones 9-6 potential problems
>>     >> 
>>     >> zhangjianguo2002 wrote:
>>     >> > Hi everyone!
>>     >> >   Have anyone used the Lennard-Jones 9-6 potential for  
>> coarse-grained 
>>     >> > models? when I use it, I get a very different result from  that is 
>> got 
>>     >> > from the same Lennard-Jones 9-6 potential  formed a potential 
>> table,the 
>>     >> > latter's results are comparable to the experiments. when I use 
>> LJ-9-6 
>>     >> > potential,the ITP file  is as following:
>>     >> >  
>>     >> >   [ defaults ]
>>     >> > ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>>     >> >    1             1               no              1.0     1.0     9
>>     >> 
>>     >> Even if this may generate the correct parameters (please use gmxdump 
>> to 
>>     >> check your tpr file) you still have to provide a user table to mdrun 
>> and 
>>     >> to set vdw-type = user in your mdp file. You may need to change the 
>>     >> nbfunc to three as well. Check source code in src/kernel/convparm to 
>> see 
>>     >> what is going on.  I don't think this is documented anywhere, is it?
>>     >> 
 
Thanks very much for your advice! According to you , I provide a user table( 
Does this mean that LJ'parameters epsilon and sigma setted in the ITP file 
don't work ? ) and set vdw-type = user as well as change nbfunc to three ,but 
grompp reports some errors that : "Invalid nonbond function selector '3' using 
LJ",I read the manual again,it says : non-bond type =1(Lennaed-Jones) or 
2(Buckingham), that is seemed that 3 is a illegal choice, is there something 
wrong?

 
>>     >> 
>>     >> > 
>>     >> > [ atomtypes ]
>>     >> > ;   name  bond_type    mass    charge   ptype          sigma      
>> epsilon
>>     >> >  opls_001   Cx  6      78.0190    0            A    0.505        
>> 2.95;
>>     >> > 
>>     >> >  [ moleculetype ]
>>     >> > ; Name nrexcl
>>     >> > Phenyl      1
>>     >> > [ atoms ]
>>     >> > ;   nr      type  resnr resid  atom  cgnr   charge     mass
>>     >> >      1     opls_001     1  Phenyl     C1     1    0.000  78.0190 
>>     >> > 
>>     >> >  other files ,such as mdp file and top file ,are all the same as 
>> normal 
>>     >> > LJ-12-6 potential, are these correct if I want to use LJ-9-6 
>> potential? 
>>     >> > Do I still need to change something? Thanks very much for your 
>> kindness!
>>     >> > 
>>     >> > 
>>     >> > 
>>     >> > 
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>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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