At 2011-01-04 16:19:05，gmx-users-requ...@gromacs.org wrote:
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>Today's Topics:
>
> 1. Re: Re: [gmx-users] Trifluoroethanol-Ethanol mixtures study
> (wibke.sudh...@cloudbroker.com)
> 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: wibke.sudh...@cloudbroker.com
>Subject: Re: Re: [gmx-users] Trifluoroethanol-Ethanol mixtures study
>To: gmx-users@gromacs.org
>Message-ID:<20110104002306.1761.qm...@server12.hostfactory.ch>
>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
i...@cloudbroker.com. In case you have any issues with the CloudBroker Platform,
please send an email to our helpdesk at platf...@cloudbroker.com. 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: i...@cloudbroker.com
>Web: http://www.cloudbroker.com
>
>
>
>
>
>------------------------------
>
>Message: 2
>Date: Tue, 04 Jan 2011 11:27:29 +1100
>From: Mark Abraham<mark.abra...@anu.edu.au>
>Subject: [gmx-users] Email bounce message
>To: Discussion list for GROMACS users<gmx-users@gromacs.org>
>Message-ID:<4d226971.8000...@anu.edu.au>
>Content-Type: text/plain; charset=UTF-8; format=flowed
>
>On 4/01/2011 11:23 AM, wibke.sudh...@cloudbroker.com 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
i...@cloudbroker.com. In case you have any issues with the CloudBroker Platform,
please send an email to our helpdesk at platf...@cloudbroker.com. 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<gtr...@gmail.com>
>Subject: [gmx-users] g_mindist
>To: gmx-users@gromacs.org
>Message-ID:
> <aanlktiktntrig9ct1zpq3ufupfoiy2pfaebta8b+t...@mail.gmail.com>
>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
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>------------------------------
>
>Message: 4
>Date: Mon, 03 Jan 2011 20:29:02 -0500
>From: "Justin A. Lemkul"<jalem...@vt.edu>
>Subject: Re: [gmx-users] g_mindist
>To: Discussion list for GROMACS users<gmx-users@gromacs.org>
>Message-ID:<4d2277de.6080...@vt.edu>
>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
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>========================================
>
>
>------------------------------
>
>Message: 5
>Date: Tue, 4 Jan 2011 11:59:53 +0530
>From: sreelakshmi ramesh<sree.laks...@research.iiit.ac.in>
>Subject: Re: [gmx-users] The sum of the O-H distancesof the backbone
> hydrogen bonds ROH
>To: Discussion list for GROMACS users<gmx-users@gromacs.org>
>Message-ID:
> <aanlktikw-m-ncbpnkaj8rxnrvjrdezypsncfmmbih...@mail.gmail.com>
>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<mark.abra...@anu.edu.au>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
>> --
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>------------------------------
>
>Message: 6
>Date: Tue, 4 Jan 2011 15:45:57 +0800 (CST)
>From: gromacs<ptf1...@163.com>
>Subject: [gmx-users] How to get sufactant.gro, sufactant.top,
>To: gmx-users@gromacs.org
>Message-ID:<7bda4963.110c4.12d4ffd516f.coremail.ptf1...@163.com>
>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
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>------------------------------
>
>Message: 7
>Date: Tue, 04 Jan 2011 19:18:10 +1100
>From: Mark Abraham<mark.abra...@anu.edu.au>
>Subject: Re: [gmx-users] How to get sufactant.gro, sufactant.top,
>To: Discussion list for GROMACS users<gmx-users@gromacs.org>
>Message-ID:<7690a1161265.4d237...@anu.edu.au>
>Content-Type: text/plain; charset="iso-8859-1"
>
>On 01/04/11, gromacs<ptf1...@163.com> 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
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
>
>
>>
>>
>> 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
>
>
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