[gmx-users] Re: gmx-users Digest, Vol 71, Issue 105

程迪 chengdi123000 at gmail.com
Tue Mar 23 12:39:54 CET 2010 

But there is still a problem: I am not building a single SiO2 molecule, but
building a Si-O amorphous network structure. Gromacs may treat it as a
single molecule...

I am checking if x2top is helpful.

I just came up a new idea: I am simulating nano SIO2 sphere's interaction
between cell membrane. Can I just treat the sphere like a rigid body, and
just consider the VDW and electric force act upon SiO2. Any internal force
and movement are ignored. And I only need to write LJ constant and charges
on every atom to the .top file.



Di Cheng

University of Science and Technology of China
Hefei, Anhui Province 230026
P. R. China
E-mail: chengdi at mail.ustc.edu.cn
Tel.: +86-15321055911



On Tue, Mar 23, 2010 at 7:00 PM, <gmx-users-request at gromacs.org> wrote:

> Send gmx-users mailing list submissions to
>        gmx-users at gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
>        gmx-users-request at gromacs.org
>
> You can reach the person managing the list at
>        gmx-users-owner at gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
>   1. Re: [help]How to produce .top file from Material Studio (Yang Ye)
>   2. Re: [help]How to produce .top file from Material  Studio
>      (szewczyk at ualberta.ca)
>   3. new/old gromacs-wiki (Christian Seifert)
>   4. Dynamics cross correlation map (sukesh chandra gain)
>   5. Re: Dynamics cross correlation map (Tsjerk Wassenaar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 23 Mar 2010 10:37:36 +0800
> From: Yang Ye <leafyoung at yahoo.com>
> Subject: Re: [gmx-users] [help]How to produce .top file from Material
>        Studio
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <1b3c3eeb1003221937r6846de78le49635f8fe76c2c4 at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> No way from MS. Check x2top.
>
> Yang YE
>
> On Mon, Mar 22, 2010 at 10:42 PM, 程迪 <chengdi123000 at gmail.com> wrote:
>
> > Hi,everyone
> >
> > I have build a SiO2 structure in Material Studio, And I've set the xyz
> > coordinates and force field parameters of the structure. Is there some
> tool
> > or method to produce a .top file from MS. I do not want to write .top
> file
> > line by line.
> >
> > Thanks.
> >
> > Di Cheng
> >
> > University of Science and Technology of China
> > Hefei, Anhui Province 230026
> > P. R. China
> > E-mail: chengdi at mail.ustc.edu.cn
> > Tel.: +86-15321055911
> >
> >
> > --
> > gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Regards,
> Yang Ye
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20100323/ee9ef0ce/attachment-0001.html
>
> ------------------------------
>
> Message: 2
> Date: Mon, 22 Mar 2010 22:54:04 -0600
> From: szewczyk at ualberta.ca
> Subject: Re: [gmx-users] [help]How to produce .top file from Material
>        Studio
> To: gmx-users at gromacs.org
> Message-ID: <20100322225404.14850saq7v861ieo at webmail.ualberta.ca>
> Content-Type: text/plain;       charset=ISO-8859-1;     DelSp="Yes";
>        format="flowed"
>
> Hi,
> I run my simulations in Gromacs but I generated my structure in
> Materials Studio as well and I agree with Yang Ye - MS will not give
> you the .top.
> It`s either x2top or by hand if your system is quite simple or if you
> can create a topology of one molecule which then can be multiplied
> with genconf and/or editconf in Gromacs.
>
> Good luck!
>
> Paula
>
>
> Quoting "Yang Ye" <leafyoung at yahoo.com>:
>
> > No way from MS. Check x2top.
> >
> > Yang YE
> >
> > On Mon, Mar 22, 2010 at 10:42 PM, ?? <chengdi123000 at gmail.com> wrote:
> >
> >> Hi,everyone
> >>
> >> I have build a SiO2 structure in Material Studio, And I've set the xyz
> >> coordinates and force field parameters of the structure. Is there some
> tool
> >> or method to produce a .top file from MS. I do not want to write .top
> file
> >> line by line.
> >>
> >> Thanks.
> >>
> >> Di Cheng
> >>
> >> University of Science and Technology of China
> >> Hefei, Anhui Province 230026
> >> P. R. China
> >> E-mail: chengdi at mail.ustc.edu.cn
> >> Tel.: +86-15321055911
> >>
> >>
> >> --
> >> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>
> >
> >
> >
> > --
> > Regards,
> > Yang Ye
> >
>
>
>
> ------------------------------
>
> Message: 3
> Date: 23 Mar 2010 11:38:42 +0100
> From: "Christian Seifert" <cseifert at bph.ruhr-uni-bochum.de>
> Subject: [gmx-users] new/old gromacs-wiki
> To: gmx-users at gromacs.org
> Message-ID: <1269340722.4755.5.camel at moganshan>
> Content-Type: text/plain
>
> Hi.
>
> I can not use the oldwiki.gromacs.org . The page seems to be down. And
> wiki.gromacs.org is a room booking system for the biophysics department
> of the University of Stockholm (showing that the CBR kitchen is booked
> for Computational protein science today^^).
>
> Greets,
> Christian
>
> --
> M.Sc. Christian Seifert
> Department of Biophysics
> University of Bochum
> ND 04/67
> 44780 Bochum
> Germany
> Tel: +49 (0)234 32 28363
> Fax: +49 (0)234 32 14626
> E-Mail: cseifert at bph.rub.de
> Web: http://www.bph.rub.de
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 23 Mar 2010 16:14:48 +0530
> From: sukesh chandra gain <sukesh at atc.tcs.com>
> Subject: [gmx-users] Dynamics cross correlation map
> To: gmx-users at gromacs.org
> Message-ID: <4BA89BA0.4070707 at atc.tcs.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear All,
>
> Could you please tell how to get the Dynamic Cross Correlation map
> with Gromacs analysis tool or other tools. I want to know over a 20 ns
> simulation whether the motions of two residues or group of residues are
> correlated or anti correlated. For this I want to plot a dynamics cross
> correlation map in which I could get the precise information of group of
> atoms.
> I have done the following step and got the covariance matrix but don't
> know how to proceed further.
>  >g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l
> covar.log -xpm covar.xpm -ascii covar.dat
> Waiting for your input.
>
> Thank You,
> Regards,
> Sukesh
>
> --
> Sukesh Chandra Gain
> TCS Innovation Labs
> Tata Consultancy Services Ltd.
> 'Deccan Park', Madhapur
> Hyderabad 500081
> Phone:  +91 40 6667 3572
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 23 Mar 2010 11:54:52 +0100
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] Dynamics cross correlation map
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <8ff898151003230354q15b3591bw2e531a1edbb8b26a at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Sukesh,
>
> You've posted this question several times now, without changing the
> phrasing. Did it occur to you that maybe nobody felt equipped to or
> sufficiently triggered by your post to reply? What do you mean with a
> 'dynamics cross correlation map' for 'residues or groups of residues'?
> Being more explicit, also pointing to some references or giving some
> formulas, might help you get a response.
> But isn't your answer already in the image covar.xpm? Otherwise, maybe
> using the atomic covariances (-xpma) might do what you want. If not,
> your problem is not as trivial as you may think.
>
> Cheers,
>
> Tsjerk
>
> On Tue, Mar 23, 2010 at 11:44 AM, sukesh chandra gain
> <sukesh at atc.tcs.com> wrote:
> > Dear All,
> >
> > Could you please tell how to get the Dynamic Cross Correlation map with
> > Gromacs analysis tool or other tools. I want to know over a 20 ns
> simulation
> > whether the motions of two residues or group of residues are correlated
> or
> > anti correlated. For this I want to plot a dynamics cross correlation map
> in
> > which I could get the precise information of group of atoms.
> > I have done the following step and got the covariance matrix but don't
> know
> > how to proceed further.
> >>g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l
> >> covar.log -xpm covar.xpm -ascii covar.dat
> > Waiting for your input.
> >
> > Thank You,
> > Regards,
> > Sukesh
> >
> > --
> > Sukesh Chandra Gain
> > TCS Innovation Labs
> > Tata Consultancy Services Ltd.
> > 'Deccan Park', Madhapur
> > Hyderabad 500081
> > Phone:  +91 40 6667 3572
> >
> > --
> > gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> Groningen Institute for Biomolecular Research and Biotechnology
> University of Groningen
> The Netherlands
>
>
> ------------------------------
>
> --
> gmx-users mailing list
> gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 71, Issue 105
> ******************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100323/13b7c1e8/attachment.html>

More information about the gromacs.org_gmx-users mailing list