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...<br><br>I am checking if x2top is helpful.<br><br>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. <br>
<br><br clear="all"><br>Di Cheng<br><br>University of Science and Technology of China<br>Hefei, Anhui Province 230026<br>P. R. China<br>E-mail: <a href="mailto:chengdi@mail.ustc.edu.cn">chengdi@mail.ustc.edu.cn</a><br>Tel.: +86-15321055911<br>
<br>
<br><br><div class="gmail_quote">On Tue, Mar 23, 2010 at 7:00 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Send gmx-users mailing list submissions to<br>
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of gmx-users digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. Re: [help]How to produce .top file from Material Studio (Yang Ye)<br>
2. Re: [help]How to produce .top file from Material Studio<br>
(<a href="mailto:szewczyk@ualberta.ca">szewczyk@ualberta.ca</a>)<br>
3. new/old gromacs-wiki (Christian Seifert)<br>
4. Dynamics cross correlation map (sukesh chandra gain)<br>
5. Re: Dynamics cross correlation map (Tsjerk Wassenaar)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 23 Mar 2010 10:37:36 +0800<br>
From: Yang Ye <<a href="mailto:leafyoung@yahoo.com">leafyoung@yahoo.com</a>><br>
Subject: Re: [gmx-users] [help]How to produce .top file from Material<br>
Studio<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:1b3c3eeb1003221937r6846de78le49635f8fe76c2c4@mail.gmail.com">1b3c3eeb1003221937r6846de78le49635f8fe76c2c4@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
No way from MS. Check x2top.<br>
<br>
Yang YE<br>
<br>
On Mon, Mar 22, 2010 at 10:42 PM, 程迪 <<a href="mailto:chengdi123000@gmail.com">chengdi123000@gmail.com</a>> wrote:<br>
<br>
> Hi,everyone<br>
><br>
> I have build a SiO2 structure in Material Studio, And I've set the xyz<br>
> coordinates and force field parameters of the structure. Is there some tool<br>
> or method to produce a .top file from MS. I do not want to write .top file<br>
> line by line.<br>
><br>
> Thanks.<br>
><br>
> Di Cheng<br>
><br>
> University of Science and Technology of China<br>
> Hefei, Anhui Province 230026<br>
> P. R. China<br>
> E-mail: <a href="mailto:chengdi@mail.ustc.edu.cn">chengdi@mail.ustc.edu.cn</a><br>
> Tel.: +86-15321055911<br>
><br>
><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br>
<br>
<br>
<br>
--<br>
Regards,<br>
Yang Ye<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20100323/ee9ef0ce/attachment-0001.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20100323/ee9ef0ce/attachment-0001.html</a><br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Mon, 22 Mar 2010 22:54:04 -0600<br>
From: <a href="mailto:szewczyk@ualberta.ca">szewczyk@ualberta.ca</a><br>
Subject: Re: [gmx-users] [help]How to produce .top file from Material<br>
Studio<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:20100322225404.14850saq7v861ieo@webmail.ualberta.ca">20100322225404.14850saq7v861ieo@webmail.ualberta.ca</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";<br>
format="flowed"<br>
<br>
Hi,<br>
I run my simulations in Gromacs but I generated my structure in<br>
Materials Studio as well and I agree with Yang Ye - MS will not give<br>
you the .top.<br>
It`s either x2top or by hand if your system is quite simple or if you<br>
can create a topology of one molecule which then can be multiplied<br>
with genconf and/or editconf in Gromacs.<br>
<br>
Good luck!<br>
<br>
Paula<br>
<br>
<br>
Quoting "Yang Ye" <<a href="mailto:leafyoung@yahoo.com">leafyoung@yahoo.com</a>>:<br>
<br>
> No way from MS. Check x2top.<br>
><br>
> Yang YE<br>
><br>
> On Mon, Mar 22, 2010 at 10:42 PM, ?? <<a href="mailto:chengdi123000@gmail.com">chengdi123000@gmail.com</a>> wrote:<br>
><br>
>> Hi,everyone<br>
>><br>
>> I have build a SiO2 structure in Material Studio, And I've set the xyz<br>
>> coordinates and force field parameters of the structure. Is there some tool<br>
>> or method to produce a .top file from MS. I do not want to write .top file<br>
>> line by line.<br>
>><br>
>> Thanks.<br>
>><br>
>> Di Cheng<br>
>><br>
>> University of Science and Technology of China<br>
>> Hefei, Anhui Province 230026<br>
>> P. R. China<br>
>> E-mail: <a href="mailto:chengdi@mail.ustc.edu.cn">chengdi@mail.ustc.edu.cn</a><br>
>> Tel.: +86-15321055911<br>
>><br>
>><br>
>> --<br>
>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
>> Please don't post (un)subscribe requests to the list. Use the<br>
>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
>><br>
><br>
><br>
><br>
> --<br>
> Regards,<br>
> Yang Ye<br>
><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: 23 Mar 2010 11:38:42 +0100<br>
From: "Christian Seifert" <<a href="mailto:cseifert@bph.ruhr-uni-bochum.de">cseifert@bph.ruhr-uni-bochum.de</a>><br>
Subject: [gmx-users] new/old gromacs-wiki<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <1269340722.4755.5.camel@moganshan><br>
Content-Type: text/plain<br>
<br>
Hi.<br>
<br>
I can not use the <a href="http://oldwiki.gromacs.org" target="_blank">oldwiki.gromacs.org</a> . The page seems to be down. And<br>
<a href="http://wiki.gromacs.org" target="_blank">wiki.gromacs.org</a> is a room booking system for the biophysics department<br>
of the University of Stockholm (showing that the CBR kitchen is booked<br>
for Computational protein science today^^).<br>
<br>
Greets,<br>
Christian<br>
<br>
--<br>
M.Sc. Christian Seifert<br>
Department of Biophysics<br>
University of Bochum<br>
ND 04/67<br>
44780 Bochum<br>
Germany<br>
Tel: +49 (0)234 32 28363<br>
Fax: +49 (0)234 32 14626<br>
E-Mail: <a href="mailto:cseifert@bph.rub.de">cseifert@bph.rub.de</a><br>
Web: <a href="http://www.bph.rub.de" target="_blank">http://www.bph.rub.de</a><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Tue, 23 Mar 2010 16:14:48 +0530<br>
From: sukesh chandra gain <<a href="mailto:sukesh@atc.tcs.com">sukesh@atc.tcs.com</a>><br>
Subject: [gmx-users] Dynamics cross correlation map<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:4BA89BA0.4070707@atc.tcs.com">4BA89BA0.4070707@atc.tcs.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
Dear All,<br>
<br>
Could you please tell how to get the Dynamic Cross Correlation map<br>
with Gromacs analysis tool or other tools. I want to know over a 20 ns<br>
simulation whether the motions of two residues or group of residues are<br>
correlated or anti correlated. For this I want to plot a dynamics cross<br>
correlation map in which I could get the precise information of group of<br>
atoms.<br>
I have done the following step and got the covariance matrix but don't<br>
know how to proceed further.<br>
>g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l<br>
covar.log -xpm covar.xpm -ascii covar.dat<br>
Waiting for your input.<br>
<br>
Thank You,<br>
Regards,<br>
Sukesh<br>
<br>
--<br>
Sukesh Chandra Gain<br>
TCS Innovation Labs<br>
Tata Consultancy Services Ltd.<br>
'Deccan Park', Madhapur<br>
Hyderabad 500081<br>
Phone: +91 40 6667 3572<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Tue, 23 Mar 2010 11:54:52 +0100<br>
From: Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
Subject: Re: [gmx-users] Dynamics cross correlation map<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:8ff898151003230354q15b3591bw2e531a1edbb8b26a@mail.gmail.com">8ff898151003230354q15b3591bw2e531a1edbb8b26a@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
Hi Sukesh,<br>
<br>
You've posted this question several times now, without changing the<br>
phrasing. Did it occur to you that maybe nobody felt equipped to or<br>
sufficiently triggered by your post to reply? What do you mean with a<br>
'dynamics cross correlation map' for 'residues or groups of residues'?<br>
Being more explicit, also pointing to some references or giving some<br>
formulas, might help you get a response.<br>
But isn't your answer already in the image covar.xpm? Otherwise, maybe<br>
using the atomic covariances (-xpma) might do what you want. If not,<br>
your problem is not as trivial as you may think.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
On Tue, Mar 23, 2010 at 11:44 AM, sukesh chandra gain<br>
<<a href="mailto:sukesh@atc.tcs.com">sukesh@atc.tcs.com</a>> wrote:<br>
> Dear All,<br>
><br>
> Could you please tell how to get the Dynamic Cross Correlation map with<br>
> Gromacs analysis tool or other tools. I want to know over a 20 ns simulation<br>
> whether the motions of two residues or group of residues are correlated or<br>
> anti correlated. For this I want to plot a dynamics cross correlation map in<br>
> which I could get the precise information of group of atoms.<br>
> I have done the following step and got the covariance matrix but don't know<br>
> how to proceed further.<br>
>>g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l<br>
>> covar.log -xpm covar.xpm -ascii covar.dat<br>
> Waiting for your input.<br>
><br>
> Thank You,<br>
> Regards,<br>
> Sukesh<br>
><br>
> --<br>
> Sukesh Chandra Gain<br>
> TCS Innovation Labs<br>
> Tata Consultancy Services Ltd.<br>
> 'Deccan Park', Madhapur<br>
> Hyderabad 500081<br>
> Phone: +91 40 6667 3572<br>
><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the www interface<br>
> or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br>
<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
Groningen Institute for Biomolecular Research and Biotechnology<br>
University of Groningen<br>
The Netherlands<br>
<br>
<br>
------------------------------<br>
<font color="#888888"><br>
--<br>
gmx-users mailing list<br>
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
<br>
End of gmx-users Digest, Vol 71, Issue 105<br>
******************************************<br>
</font></blockquote></div><br>