[gmx-users] Re: A very good morning Sir

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 11 13:43:50 CEST 2011

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor.  I am CC'ing this message to the list and would ask that all 
further discussion be posted there.  Comments embedded below.

Sabitoj Singh Virk wrote:
> Hello,
> It could be really helpful of a person like you with  such high 
> expertise to give me some insight in a problem i am facing while working 
> in gromacs.Sir, I am trying to simulate a protein in buffer conditions ( 
> Phosphate Buffer saline) whose conc. is : 137mM NaCl + 2.7 mM KCl + 
> 10.15 mM Na2HPo4 + 1.76 mM KH2Po4 . I have tried almost many ways to 
> incorporate more than one salt in the solvent box but in vain. ' Genion 
> ' command does not work after one salt has been added (i.e only NaCl is 
> added using -conc option and no other salt).If 'Genion' command is 
> executed again,it shows : " No ions to add and no potential to calculate ".

The only way to build such a complex system is to manually specify the number of 
each ion or molecule to be added to the system.  Add your polyatomic ions first 
with genbox -ci -nmol, then solvate and add NaCl and KCl.  You will have to use 
the -np and -nn flags with genion.  A simple calculation based on the box volume 
will tell you how many ions to use.  Do not be surprised if you cannot get 
exactly the right concentration without using a horrendously large box.  Such 
small concentrations make it difficult to prepare the MD system exactly like the 
experiment and you may have to do a bit of rounding.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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