[gmx-users] Fw:Re: on CHARMM-GUI produced lipid bilayer for gromacs use

[Tsjerk Wassenaar]

Brett,

Please do not mail me directly with such questions. I am not your tutor and
I am not involved in the CHARMM-GUI. I forward this mail to the gromacs
user list, as there may be someone who can and is willing to give
suggestions there. But I do also like to note that the CHARMM-GUI is not
Gromacs and that it may be better to contact the authors there or to see if
they have a user forum.

Cheers,

Tsjerk

On Thu, Sep 17, 2015 at 9:51 AM, Brett <brettliu123 at 163.com> wrote:

> Dear Tsjerk,
>
> Thanks for your reply. When using CHARM-GUI lipid bilayer builder, I have
> met the following problems, which I hope you can answer.
>
> For step 1, there is "Generate Pore Water and Measure Pore Size". What is
> the function of "Generate Pore Water and Measure Pore Size"? Should I click
> it or not?
>
> For step 2, thers is "determines system size based on lipid layers between
> neighboring proteins (default 1.5)". Where there are lipid bilayers between
> neighboring proteins? I think the lipid bilayer should only exist in the
> trans-membrane part of the membrane protein.
>
> For step 3, there is "Check lipid ring (and protein surface) penetration
> "? What is this for? Should I click it or not?
>
> For step 5, there is "NPT ensemble ", “NPAT ensemble”and “NPgT ensemble”.
> I regard the "NPT" has the same meaning as the "MPT" used in gromacs
> on-line tutorial, then what is “NPAT ensemble”and “NPgT ensemble”?
>
> For step 6, in step 5 I have selected "NPT ensemble" and I only select
> gromacs output. Attached image was the snapshort of the results from step
> 6. It seems it did not contain the the .top file as you mentoned in youe
> e-mail. Did I do something wrong?
>
> Next step, if for the PDB as mentioned in the attached snapshort image, I
> delete all the H2O, and then I start it with the H2O deleted PDB fom the
> pdb2gmx step, in the step to add water box, it is rather clear water will
> be added and in the surronding edge of the lipid, how the gromacs process
> the contact between water and the lipid tail of the lipid bilayer?
>
> I am looking forward to getting a reply from you.
>
> Best regards.
>
> Brett
>
>
>
>
>
>
>
> -------- Forwarding messages --------
> From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> Date: 2015-09-17 13:57:37
> To:  "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] on CHARMM-GUI produced lipid bilayer for gromacs use
> Hi Brett,
>
> The CHARMM-GUI also provides the .top file. You can use that and the PDB
> (it doesn't need to be .gro) to run grompp.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Sep 17, 2015 at 5:06 AM, Brett <brettliu123 at 163.com> wrote:
>
> > Dear All,
> >
> >
> > After I got the membrane protein PDB with the membrane part packed in
> > lipid bilayer by the lipid bilayer builder of CHARMM-GUI, will you please
> > let me know how to get the inputs for the gromacs next step MD process？ For
> > example， if I wand to go directly to the nvt equilibration step with the
> > CHARMM-GUI produced PDB, the command in the lysozyme tutorial is "gmx
> > grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr". Then will you please
> > let me know how to get the input *.gro and *.top file in order to get the
> > *.tpr file? Or for the  CHARMM-GUI produced PDB, I delete all the H2O, and
> > then start from the pdb2gmx step with the PDB file containing only the
> > membrane protein and the lipid bilayer? But in this way it seems the sides
> > of the lipid bilayer will also be packed in H2O.
> >
> >
> > I am looking forward to getting a reply from you.
> >
> >
> > Best regards.
> >
> >
> > Brett
> >
> >
> >
> >
> >
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>
>
>
>
>



-- 
Tsjerk A. Wassenaar, Ph.D.