[gmx-users] regarding nacl simulation in water using tabulated potentials

[sreelakshmi ramesh]

Dear Mark,
                 i followed the same stuff in the tutoriali created the
table and tried the following command
*
grompp -f  em.mdp -p tol.top -c nacl3.pdb*
i got the following etrrors

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#

WARNING 1 [file tol.top, line 8]:
  Too few parameters on line (source file toppush.c, line 315)


WARNING 2 [file tol.top, line 9]:
  Too few parameters on line (source file toppush.c, line 315)


ERROR 1 [file tol.top, line 13]:
  Invalid directive nonbond params


WARNING 3 [file tol.top, line 15]:
  Too few parameters on line (source file toppush.c, line 315)





On Tue, May 10, 2011 at 4:25 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 10/05/2011 2:20 AM, sreelakshmi ramesh wrote:
>
> i had three tables one for solvent na and solvent cl ions (obeying lj
> potential) and na ,cl obeying my own potential.i have the following mdp file
>
> em.mdp
> title = nacl
> cpp = /usr/bin/cpp ; the c preprocessor
> define= -DEFLEXIBLE
> integrator = md
> dt = 0.001 ; ps !
> nsteps = 60000
> nstlist = -1
> ns_type = grid
> rlist = 1.4
> coulombtype = user
> rcoulomb = 1.0
> energygrps = Na Cl Sol
> energygrp_table = Na Cl Na Sol Cl Sol
>
>
> If your mdrun -table file will be for LJ, then the only tables you need to
> specify here are for Na-Cl interactions.
>
>
>  rvdw = 1.0
> vdwtype= user
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> pbc=xyz;
> ; Energy minimizing stuff
> emtol = 1000.0
> emstep = 0.01
>
>
> *and topology file is as follows*
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ  fudgeQQ
>    1        1         yes      0.5      0.8333
>
>
> [ atomtypes ]
> ; name bond type mass charge ptype C A
>   Na    Na   22.99      1   A   1.0e-03
>   Cl    Cl   35.453    -1   A   9.0e-06
>
>
>
> [ nonbond params ]
> ;i j  func   A           B               C
> Na Cl 1   2.01E-09       3.154          11.2E-12   (buckingham)
>
> I dont have idea how to include water topology and include  A B paramaters
> for water-ion interaction (lennard jones)
>
>
> Set up a normal aqueous Na Cl simulation and adapt that. Consult tutorial
> material for examples for including water.
>
> See http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials,
> like I suggested you search for earlier...
>
> Mark
>
>
>
>
> any help appreciated,
> sree lakshmi
>
> On Mon, May 9, 2011 at 12:37 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>
>>  On 9/05/2011 4:01 PM, sreelakshmi ramesh wrote:
>>
>> i had followed the instructions in themnaual for ninbonded interactions
>> adn had created two tables one for nacl adn other table for water ion
>> interations...
>>
>>
>>  That's not "I really don't  have any idea on how to do this". Please ask
>> the question you want answered, or you're wasting everyone's time.
>>
>>
>> i wanted some information on how to use these tables for starting thee
>> simulation
>>
>>
>>  Sorry, that's too general. You might want help with a command line, or
>> setting up the .mdp, or something else. Please read 6.7 of the manual, try
>> things, and ask a focused question.
>>
>> Mark
>>
>>
>>  On Mon, May 9, 2011 at 11:20 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>>
>>> On 9/05/2011 3:46 PM, sreelakshmi ramesh wrote:
>>>
>>>> dear gmx users,
>>>>                        i have to simulate nacl in water...the system is
>>>> acubic box with just one na adn one cl ion in tip3p water.i wanted to use a
>>>>  buckingham potential  for na adn cl interaction and lennard jones for water
>>>> -ion intercation.i really dont have any idea on how to do this.any help will
>>>> be of great use  for me...
>>>>
>>>
>>>  Can't be done simply. You'd have to use non-bonded interaction tables
>>> for the Na-Cl interaction with properly constructed energy groups. Search
>>> the manual and webpage for details.
>>>
>>> Mark
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>>
>>
>>
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>
>
>
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