Re: [gmx-users] How to deal with the top files

2010-04-10 Thread Justin A. Lemkul
kecy...@sina.com wrote: Hello，I have one box,which has two kinds of solvents and two kinds of solutes. How can I put the infermation of them in one top fles, Please see Chapter 5 for topology specifications, as well as: http://www.gromacs.org/Documentation/Include_File_Mechanism or w

[gmx-users] How to deal with the top files

2010-04-10 Thread kecy_wu
 Hello，I have one box,which has two kinds of  solvents and two kinds of solutes. How can I  put  the infermation  of them in one top fles, or what shall I do  to Setup the energy minimization, for the infermation is not in the same top file ?   Thank you !  -- gmx-users mailing listgmx-use

Re: [gmx-users] non-integral charge on my modeled protein structure

2010-04-10 Thread Mark Abraham
On 10/04/2010 5:06 PM, sonali dhindwal wrote: Sorry to bother you again but can you please help me in knowing "termini", The ends of polymers often need special treatment. Go and see what you've chosen and what makes sense to choose. I think total charge (i.e, cumulative) is wriiten at the

Re: [gmx-users] non-integral charge on my modeled protein structure

2010-04-10 Thread sonali dhindwal
Sorry to bother you again but can you please help me in knowing "termini", I think total charge (i.e, cumulative) is wriiten at the last residue of a protein in [atoms] part of a .top file. that is what i have pasted in my previous mail. and Mg is in my protein, that is why it is there in topolo