Hello Mark, Thank you for your reply. AS for the steps you mentioned to solvate a molecule: I have a simple molecule replicated by genconf -nbox in one direction. When I try to energy minimize this single molecule grompp em gives error: rlist is longer than half box size or longer than shortest diagnal boz size... I increase the size and everything is fine but can you please tell me what is the criterion to specify the size. Does boxsize affect results in MD? ( I am asking this because if I want to use genconf to replicate this molecule which is in a large boxzise the final size of the system can become very large so I have to use editconf to reduce the size again)
Also sometimes some parts of the molcule in the box are outside the box when I see the trajectory (ngmx) at the beginning.. and I think because of the pbc it jups inthebox from the otherside. Should the particle be entirely in box at the beginning? Thanks, On 8 July 2010 01:47, Mark Abraham <mark.abra...@anu.edu.au> wrote: > Please start new emails for new discussion topics. That way you increase > the chance that people with the interest and expertise can use their time > efficiently, and that you get an answer. Also, archives work better if you > separate topics. > > > Please Let me ask two more simple questions about solvating a molecule. > I am using genbox to solvate a solute. I have solute.gro and solvent.gro. > What should be the dimension of box in solvent.gro if i want to put -nmol > numbers in the solute box. Does it matter what size the box of solvent is > (last line in gro)? > > I don't think you are using the right tool for your problem, but your > description is so opaque it's hard to tell. genbox -nmol will try to fill > interstices, which need to exist for it to do any good. That means you need > to have prepared your solvent.gro with your solute in mind. > > > I have solvated the solute with 50 moleecules of solvent. I have the > structure file obtained from genbox. To run em or MD I need to have top > file. so I am using pdb2gmx and I get a top file for the solute and 50 > solvents but I have one moleculetype (named protein by default). I am > confused If I need to have 2 molecuels types for solute and solvent, also if > I need to enter the number of solvent molecules at the end of the top file > [mols] option, or what I have now is fine and I can proceed to em and md > usuing mdp files? :) > > 1. use pdb2gmx on an unsolvated .gro to get your protein .top > 2. use editconf to set the simulation box how you want it > 3. use genbox -p to add solvent and take care of modifying your .top > (unless your solvent is not water, in which case you'll probably have to do > some manual editing of your .top) > 4. grompp and mdrun > > Perhaps doing some tutorial material will make this and other workflows > more readily understood? > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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