[gmx-users] regarding nacl simulation in water using tabulated potentials
Mark Abraham
Mark.Abraham at anu.edu.au
Tue May 10 12:11:16 CEST 2011
On 10/05/2011 1:04 PM, sreelakshmi ramesh wrote:
> 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)
So either you're wrong or the tutorial's wrong. How can anybody here
tell? Only you can look at the lines of tol.top and see why grompp
doesn't like them...
Mark
> On Tue, May 10, 2011 at 4:25 AM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto: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 <mailto: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 <mailto: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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