<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
On 5/01/2011 5:37 PM, gromacs wrote:<br>
<br>
When replying to a list digest please do two things: correct the
subject to something appropriate (as you have done) and delete the
other posts in the digest, so that archival software doesn't get
confused about content.<br>
<br>
<blockquote
cite="mid:39d77c.75cc.12d54e5105e.Coremail.ptf1242@163.com"
type="cite">
<div>Sorry, i write wrong.</div>
<div> </div>
<div>Someone said that we cannot get sufactant.gro and sufactant.top through pdb2gmx() sufactant.pdb. Because grompp .pdb could mainly use for macro-biology big moleculars, which means some proteins etc.</div>
</blockquote>
<br>
Correct. pdb2gmx builds topologies only for some biopolymers for
which it has monomers in its database.<br>
<br>
<blockquote
cite="mid:39d77c.75cc.12d54e5105e.Coremail.ptf1242@163.com"
type="cite">
<div> So that means we could not get correct .gro, .top small molecules such as inorganic or small organic molecules (such as ethanol)
by using pdb2max command. </div>
<div> </div>
<div>Maybe we could get get sufactant.gro, sufactant.top through
the following? <a moz-do-not-send="true"
title="Downloads/Related Software/SwissParam"
href="http://www.gromacs.org/Downloads/Related_Software/SwissParam"
rel="internal">SwissParam</a> (for CHARMM forcefield), <a
moz-do-not-send="true" title="Documentation/Commands/PRODRG"
href="http://www.gromacs.org/Downloads/Related_Software/PRODRG"
rel="internal">PRODRG</a> (for ffgmx/GROMOS96 43A1), <a
moz-do-not-send="true" title="Downloads/Related
Software/Automated Topology Builder"
href="http://www.gromacs.org/Downloads/Related_Software/Automated_Topology_Builder"
rel="internal">Automated Topology Builder</a> (for GROMOS96
53A6), <a moz-do-not-send="true"
title="Documentation/Commands/MKTOP"
href="http://www.gromacs.org/Downloads/Related_Software/MKTOP"
rel="internal">MKTOP</a> (for OPLS/AA)<br>
?</div>
<div>But how can we get surfactant such as SDS .gro?<br>
</div>
</blockquote>
<br>
Some of those sources will build a coordinate file as well. Other
sources might be found here
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/File_Formats/Coordinate_File">http://www.gromacs.org/Documentation/File_Formats/Coordinate_File</a><br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:39d77c.75cc.12d54e5105e.Coremail.ptf1242@163.com"
type="cite">
<div><br>
</div>
<br>
<pre>
At 2011-01-04 16:19:05，<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> wrote:
>Send gmx-users mailing list submissions to
> <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
>
>To subscribe or unsubscribe via the World Wide Web, visit
> <a class="moz-txt-link-freetext" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a>
>or, via email, send a message with subject or body 'help' to
> <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>
>
>You can reach the person managing the list at
> <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</a>
>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of gmx-users digest..."
>
>
>Today's Topics:
>
> 1. Re: Re: [gmx-users] Trifluoroethanol-Ethanol mixtures study
> (<a class="moz-txt-link-abbreviated" href="mailto:wibke.sudholt@cloudbroker.com">wibke.sudholt@cloudbroker.com</a>)
> 2. Email bounce message (Mark Abraham)
> 3. g_mindist (Ramachandran G)
> 4. Re: g_mindist (Justin A. Lemkul)
> 5. Re: The sum of the O-H distancesof the backbone hydrogen
> bonds ROH (sreelakshmi ramesh)
> 6. How to get sufactant.gro, sufactant.top, (gromacs)
> 7. Re: How to get sufactant.gro, sufactant.top, (Mark Abraham)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: 4 Jan 2011 01:23:06 +0100
>From: <a class="moz-txt-link-abbreviated" href="mailto:wibke.sudholt@cloudbroker.com">wibke.sudholt@cloudbroker.com</a>
>Subject: Re: Re: [gmx-users] Trifluoroethanol-Ethanol mixtures study
>To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
>Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:20110104002306.1761.qmail@server12.hostfactory.ch"><20110104002306.1761.qmail@server12.hostfactory.ch></a>
>Content-Type: text/plain; charset="UTF-8"
>
>Dear Email Sender,
>
>Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Monday, January 10, 2011.
>
>For all questions about CloudBroker, please contact the company under <a class="moz-txt-link-abbreviated" href="mailto:info@cloudbroker.com">info@cloudbroker.com</a>. In case you have any issues with the CloudBroker Platform, please send an email to our helpdesk at <a class="moz-txt-link-abbreviated" href="mailto:platform@cloudbroker.com">platform@cloudbroker.com</a>. If you need to talk to me in person for urgent or important issues, please call my mobile phone number.
>
>Kind regards,
>
>Wibke Sudholt
>
>
>--
>Dr. Wibke Sudholt
>Associate and Chair of the Management
>CloudBroker GmbH
>Technoparkstrasse 1
>CH-8005 Zurich
>Switzerland
>Phone: +41 44 633 79 34
>Email: <a class="moz-txt-link-abbreviated" href="mailto:info@cloudbroker.com">info@cloudbroker.com</a>
>Web: <a class="moz-txt-link-freetext" href="http://www.cloudbroker.com">http://www.cloudbroker.com</a>
>
>
>
>
>
>------------------------------
>
>Message: 2
>Date: Tue, 04 Jan 2011 11:27:29 +1100
>From: Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a>
>Subject: [gmx-users] Email bounce message
>To: Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
>Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:4D226971.8000808@anu.edu.au"><4D226971.8000808@anu.edu.au></a>
>Content-Type: text/plain; charset=UTF-8; format=flowed
>
>On 4/01/2011 11:23 AM, <a class="moz-txt-link-abbreviated" href="mailto:wibke.sudholt@cloudbroker.com">wibke.sudholt@cloudbroker.com</a> wrote:
>> Dear Email Sender,
>>
>> Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Monday, January 10, 2011.
>>
>> For all questions about CloudBroker, please contact the company under <a class="moz-txt-link-abbreviated" href="mailto:info@cloudbroker.com">info@cloudbroker.com</a>. In case you have any issues with the CloudBroker Platform, please send an email to our helpdesk at <a class="moz-txt-link-abbreviated" href="mailto:platform@cloudbroker.com">platform@cloudbroker.com</a>. If you need to talk to me in person for urgent or important issues, please call my mobile phone number.
>
>Can we unsubscribe this email address please? I've now had a slew of
>bounces from them.
>
>Thanks,
>
>Mark
>
>
>------------------------------
>
>Message: 3
>Date: Mon, 3 Jan 2011 17:20:23 -0800
>From: Ramachandran G <a class="moz-txt-link-rfc2396E" href="mailto:gtrama@gmail.com"><gtrama@gmail.com></a>
>Subject: [gmx-users] g_mindist
>To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
>Message-ID:
> <a class="moz-txt-link-rfc2396E" href="mailto:AANLkTiktntrig9cT1zpQ3uFUPfOiY2pfAEbTA8B+thb4@mail.gmail.com"><AANLkTiktntrig9cT1zpQ3uFUPfOiY2pfAEbTA8B+thb4@mail.gmail.com></a>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Hi Gromacs users,
> I used g_mindist to calculate the minimum distance between a residue and
>a group of water molecules.
>Since distance is a length between two points in space, for the program
>considers the bunch of water molecules(15 number)
>what specific point does the group consider ? Thank you.
>
>Yours sincerely,
>Rama
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL: <a class="moz-txt-link-freetext" href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20110103/2a4eb0bf/attachment-0001.html">http://lists.gromacs.org/pipermail/gmx-users/attachments/20110103/2a4eb0bf/attachment-0001.html</a>
>
>------------------------------
>
>Message: 4
>Date: Mon, 03 Jan 2011 20:29:02 -0500
>From: "Justin A. Lemkul" <a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a>
>Subject: Re: [gmx-users] g_mindist
>To: Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
>Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:4D2277DE.6080008@vt.edu"><4D2277DE.6080008@vt.edu></a>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
>Ramachandran G wrote:
>> Hi Gromacs users,
>> I used g_mindist to calculate the minimum distance between a residue
>> and a group of water molecules.
>> Since distance is a length between two points in space, for the program
>> considers the bunch of water molecules(15 number)
>> what specific point does the group consider ? Thank you.
>>
>
>The distance measured is that between the two closest atoms, whichever those may
>be. Read the first few sentences of g_mindist -h.
>
>-Justin
>
>> Yours sincerely,
>> Rama
>>
>>
>>
>
>--
>========================================
>
>Justin A. Lemkul
>Ph.D. Candidate
>ICTAS Doctoral Scholar
>MILES-IGERT Trainee
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
><a class="moz-txt-link-freetext" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a>
>
>========================================
>
>
>------------------------------
>
>Message: 5
>Date: Tue, 4 Jan 2011 11:59:53 +0530
>From: sreelakshmi ramesh <a class="moz-txt-link-rfc2396E" href="mailto:sree.lakshmi@research.iiit.ac.in"><sree.lakshmi@research.iiit.ac.in></a>
>Subject: Re: [gmx-users] The sum of the O-H distancesof the backbone
> hydrogen bonds ROH
>To: Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
>Message-ID:
> <a class="moz-txt-link-rfc2396E" href="mailto:AANLkTikw-M-NCBpnkAj8RxnrVjrDEzYPsNCfmMbiHV0V@mail.gmail.com"><AANLkTikw-M-NCBpnkAj8RxnrVjrDEzYPsNCfmMbiHV0V@mail.gmail.com></a>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Thanks a lot for your reply..
>
>On Mon, Jan 3, 2011 at 6:07 PM, Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a>wrote:
>
>> On 2/01/2011 2:18 PM, sreelakshmi ramesh wrote:
>>
>>> Dear all,
>>> I have a protein in water and i have simulated it for few
>>> nanoseconds and i now i wanted to monitor the The sum of the O-H distances
>>> (in Å) of the backbone
>>> hydrogen bonds ROH:i dono how to extract the value from the trajectory
>>> file.Any siuggestion please.Thanks in advance
>>>
>>
>> Look in section 7.4 of the manual for a suitable tool for extracting the
>> raw distances. You'll need some other non-GROMACS tool to add them up.
>>
>> Mark
>> --
>> gmx-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
>> <a class="moz-txt-link-freetext" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a>
>> Please search the archive at
>> <a class="moz-txt-link-freetext" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!
>> Please don't post (un)subscribe requests to the list. Use the www interface
>> or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
>> Can't post? Read <a class="moz-txt-link-freetext" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a>
>>
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL: <a class="moz-txt-link-freetext" href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20110104/fd6404ca/attachment-0001.html">http://lists.gromacs.org/pipermail/gmx-users/attachments/20110104/fd6404ca/attachment-0001.html</a>
>
>------------------------------
>
>Message: 6
>Date: Tue, 4 Jan 2011 15:45:57 +0800 (CST)
>From: gromacs <a class="moz-txt-link-rfc2396E" href="mailto:ptf1242@163.com"><ptf1242@163.com></a>
>Subject: [gmx-users] How to get sufactant.gro, sufactant.top,
>To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
>Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:7bda4963.110c4.12d4ffd516f.Coremail.ptf1242@163.com"><7bda4963.110c4.12d4ffd516f.Coremail.ptf1242@163.com></a>
>Content-Type: text/plain; charset="gbk"
>
>Hi expert,
>
>I'd like to add sufactant to water. That means i should first get the sufactant.gro, and sufactant.top.
>
>Someone said that we cannot get sufactant.gro and sufactant.top through grompp () sufactant.pdb. Because grompp .pdb could mainly use for macro-biology big moleculars, which means some proteins etc.
>So that means we could not get correct .gro, .top small molecules such as inorganic or small organic molecules (such asethanol).
>
>So how can we get the sufactant.gro, sufactant.top? and which force field should we choose for ordinary simulation? I know we often use ffoplass force field for solution.
>
>Tiefeng
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL: <a class="moz-txt-link-freetext" href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20110104/7ebcc6f6/attachment-0001.html">http://lists.gromacs.org/pipermail/gmx-users/attachments/20110104/7ebcc6f6/attachment-0001.html</a>
>
>------------------------------
>
>Message: 7
>Date: Tue, 04 Jan 2011 19:18:10 +1100
>From: Mark Abraham <a class="moz-txt-link-rfc2396E" href="mailto:mark.abraham@anu.edu.au"><mark.abraham@anu.edu.au></a>
>Subject: Re: [gmx-users] How to get sufactant.gro, sufactant.top,
>To: Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
>Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:7690a1161265.4d237272@anu.edu.au"><7690a1161265.4d237272@anu.edu.au></a>
>Content-Type: text/plain; charset="iso-8859-1"
>
>On 01/04/11, gromacs <a class="moz-txt-link-rfc2396E" href="mailto:ptf1242@163.com"><ptf1242@163.com></a> wrote:
>> Hi expert,
>>
>>
>>
>> I'd like to add sufactant to water. That means i should first get the sufactant.gro, and sufactant.top.
>>
>>
>
>No, you need a coordinate file for the starting point for your GROMACS work, and the pieces to combine into a .top. That might mean a coordinate file of all your surfactant molecules and matching .top file that you then solvate with genbox. Or you might want to use genconf to replicate some existing coordinate file somehow. Or you might have your starting point already and need to match a .top to it.
>
>
>>
>> Someone said that we cannot get sufactant.gro and sufactant.top through grompp () sufactant.pdb. Because grompp .pdb could mainly use for macro-biology big moleculars, which means some proteins etc.
>>
>>
>
>Well they (or your account of them) is wrong on what might be several points. Someone needs to understand GROMACS workflows better - perhaps by doing some tutorial material and/or reading <a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation">http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation</a>
>
>
>>
>>
>> So that means we could not get correct .gro, .top small molecules such as inorganic or small organic molecules (such as ethanol).
>>
>>
>>
>> So how can we get the sufactant.gro, sufactant.top?
>>
>>
>
>That varies widely with what raw materials exist and what the objective is.
>
>
>> and which force field should we choose for ordinary simulation? I know we often use ffoplass force field for solution.
>>
>>
>
>That's your homework, I'm afraid. See above link.
>
>Mark
>
>
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL: <a class="moz-txt-link-freetext" href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20110104/2ea4f216/attachment.html">http://lists.gromacs.org/pipermail/gmx-users/attachments/20110104/2ea4f216/attachment.html</a>
>
>------------------------------
>
>--
>gmx-users mailing list
><a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
><a class="moz-txt-link-freetext" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a>
>Please search the archive at <a class="moz-txt-link-freetext" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!
>
>End of gmx-users Digest, Vol 81, Issue 15
>*****************************************
</pre>
<br>
<br>
<span title="neteasefooter"><span id="netease_mail_footer"></span></span></blockquote>
<br>
</body>
</html>