VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Oct 19 2016 - 20:18:04 CDT

I’m not sure what you mean by adding the force field. I assume what you mean is having a valid structure file (psf). Whether or not you still have a valid psf after adding additional water depends on how you added the water. If you did it using the vmd solvate plugin, for example, it should be fine. What you always have to do is have a valid structure file that matches your coordinates.

> On Oct 19, 2016, at 6:47 PM, Life Sciences Inc <contact.lifesciences.inc_at_gmail.com> wrote:
>
> Basically I had a system who I was simulating already (lipids + water ) so I added force field and created psf and pdb, then later on I felt to add more water in the already running system I stopped simulating it and then added more water, by seeing different tutorials I noticed that yes Solvation should be the next step after running autopsf (and also it takes long time) but I was afraid that as I have added new water molecules so I have to again add force field, thats why I added water molecules first and then run autopsf to add forcefield and to get new psf and pdb files (but the screen is getting held without any response, I tried with ions and water.str file combined with force field then autopsf is running and making the psf and pdb files, but also deleting many of the water molecules)
>
> for future reference:
>
> that means I don't have to add force field again whenever I am just adding new water molecules in the system ? I have to add force field when I add protein or some other molecule, is that right ?
>
> On Wed, Oct 19, 2016 at 11:33 PM, Life Sciences Inc <contact.lifesciences.inc_at_gmail.com> wrote:
> Basically I had a system who I was simulating already (lipids + water ) so I added force field and created psf and pdb, then later on I felt to add more water in the already running system I stopped simulating it and then added more water, by seeing different tutorials I noticed that yes Solvation should be the next step after running autopsf (and also it takes long time) but I was afraid that as I have added new water molecules so I have to again add force field, thats why I added water molecules first and then run autopsf to add forcefield and to get new psf and pdb files (but the screen is getting held without any response, I tried with ions and water.str file combined with force field then autopsf is running and making the psf and pdb files, but also deleting many of the water molecules)
>
> for future reference:
>
> that means I don't have to add force field again whenever I am just adding new water molecules in the system ? I have to add force field when I add protein or some other molecule, is that right ?
>
> On Wed, Oct 19, 2016 at 9:25 PM, Peter Freddolino <petefred_at_umich.edu> wrote:
> When you say that it is getting held, is there any output going to the console? Do you have an hourglass/spinning lollipop/busy indicator for your mouse cursor when vmd is active? How long have you waited?
> The ideal workflow is to run autopsf and THEN run solvate. Autopsf will take a LONG time on a solvated system because it has to run chain splitting on all of the waters…
>
> Best,
> Peter
>
> > On Oct 19, 2016, at 12:13 PM, Life Sciences Inc <contact.lifesciences.inc_at_gmail.com> wrote:
> >
> > HI ALL
> >
> > I am trying to create a psf file and pdb file from autopsf , I am addding the charmm 36 force field for lipid and water molecules through topology file "top_all36_lipid.rtf". First I did solvation using Solvate tool of vmd and then I am loading the pdb file from solvate tool to be used in autopsf tool.
> >
> > Autopsf is making chains and everything is normal, but when the processing comes to the last chains of TIP3 water molecules somehow the tool is getting held and showing no error. I am using VMD 1.9.2 version.
> >
> > Is there any solution for this?
> >
> > Thanks
> >
> >
> >
>
>
>