[gmx-users] coarse-grained model

[Yang Ye]

Dongsheng Zhang wrote:
> Yang Ye,
>
> I am sorry to tell you I am not clear yet. Do you think I need to
> specify energygrps and corresponding energygrp_table? 
>
> If so, then I got any error message. gp1 includes atom A, and gp3
> includes atom A and B. Gromacs will complain that atoma has been in two
> groups. Each group uses it own different table, but the group members
> are overlapping bwteen some groups. How can I fix it?
>   
You don't need to define 1-4 group again. with -table and -tablep for 
mdrun, between energy group A and B, 1-2 interaction will be looked up 
from table_A_B.xvg and 1-4 interaction will be looked up from 
tablep_A_B.xvg.

And also, energygrps shall corresponds to energygrp_table.

So, instead to have

energygrps = gp1 gp2 gp3 gp4 gp5 gp6 ... gp12
energygrp_table = A A B B C C A B A C B C A14 A14 B14 B14 C14 C14 A14
B14 A14 C14 B14 C14 

You shall have

energygrps = A B C ...
energygrp_table = A A B B C C A B A C B C 

> If not, I really have concern how gromacs knows to look for
> table_A_A.xvg when it calculates A-A nonbonded interaction and look for
> table_A14_A14.xvg when it calculates 1-4 interaction between A and A
> monomers. 
>
> Could you please give me more instruction? Thank you for your help!
>
>
> Dongsheng
>
>
> On Wed, 2006-07-12 at 11:18 +0800, Yang Ye wrote:
>   
>> Don't worry about that.
>> mdrun -tablep {tablep} will follow the scheme {tablep}_A_A.xvg, 
>> {tablep}_B_B.xvg ...
>> {tablep} may be replaced by your own filename.
>>
>> Yang Ye
>>
>> Dongsheng Zhang wrote:
>>     
>>> Yang ye,
>>>
>>> Thank you very much.
>>>
>>> I have three different monomers in my system, so I have 6 different
>>> regular VMDs and 6 different 1-4 interactions. Could you please tell me
>>> how to organize those table.xvg files?
>>>
>>> energygrps = gp1 gp2 gp3 gp4 gp5 gp6 ... gp12
>>> energygrp_table = A A B B C C A B A C B C A14 A14 B14 B14 C14 C14 A14
>>> B14 A14 C14 B14 C14 
>>>
>>> If I set as the above, I wonder how gromacs know the last 6 table is for
>>> 1-4 interaction.
>>>
>>> All the best!
>>>
>>> Dongsheng
>>>
>>> On Wed, 2006-07-12 at 09:54 +0800, Yang Ye wrote:
>>>   
>>>       
>>>> mdrun -tablep
>>>>
>>>> Dongsheng Zhang wrote:
>>>>     
>>>>         
>>>>> Hello, GMX users,
>>>>>
>>>>> I have a coarse-grained model. Both 1-4 and regular vdw interaction are
>>>>> tabulated, but no electrostatic interaction. Since there is no entry for
>>>>> 1-4 interaction in energy_table. I am thinking to fool gromacs by
>>>>> treating 1-4 interactions as electrostatic interactions, in other words,
>>>>> every time when 1-4 interaction energy needed, I will ask gromacs to
>>>>> calculate COUL energy by reading energy_table. Does anyone know where
>>>>> 1-4 interaction is calculated and how I can switch it to calculate COUL
>>>>> energy in the source code? Any help will be highly appreciated!
>>>>>
>>>>>
>>>>> All the best!
>>>>>
>>>>>
>>>>> Dongsheng
>>>>> _______________________________________________
>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please don't post (un)subscribe requests to the list. Use the 
>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>>
>>>>>   
>>>>>       
>>>>>           
>>>> _______________________________________________
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>> Please don't post (un)subscribe requests to the list. Use the 
>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>     
>>>>         
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please don't post (un)subscribe requests to the list. Use the 
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>   
>>>       
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the 
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>     
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>