From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Tue Jul 22 2014 - 23:04:23 CDT
Following points I need your views:
1. First thing is that I am willing to learn NAMD and related MD skills for my research work, although my lab do not have subsequent knowledge about it, but still this one of the powerful tool for research work.
2. If you demotivate everyone like this than in future the NAMD user number will be effected.
3. NAMD should provide all the relevant solution for the users in both the commercial and academic versions because I am not in condition to purchase the software, that means I can't do the things, but I want to the MDS and want to build the force field for my molecule.
4. I want to know how to do this possible task in your way, and as you mentioned about the training I request you to please help me out for the training thing, I will be lucky to get training under your supervision.
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Axel Kohlmeyer <akohlmey_at_gmail.com>
Sent: Wednesday, July 23, 2014 12:14 AM
To: Kenno Vanommeslaeghe
Subject: Re: namd-l: Force field design
On Tue, Jul 22, 2014 at 11:40 AM, Kenno Vanommeslaeghe
> Dear Abishek,
> In that case, you should try to make your prof read this:
> He or she basically gave you an impossible task. I don't want to discourage
i would not only call this an impossible task, but also outright
irresponsible behavior of the PI. not only to his student, but the
community in general. i can only encourage students to own up to this
and *demand* to be properly trained. it is not the job of the
community to compensate for this, especially when this is piled on top
of software and parameters that are provided at no cost and contain
the collected knowledge and experience of many, many people. PIs
exhibiting such irresponsible behavior should be named in public so
that a) students are made aware of the risk they may be taking and b)
their publications including simulation data, can be put under
particularly close scrutiny, since they are likely to be faulty and
> you, but it's the truth. Even if after a lot of sweat and tears, you somehow
> succeed to get a result out of NAMD, it will be hard to make sure you
> avoided all the nontrivial pitfalls and your results are relevant.
> On 07/22/2014 06:33 AM, Abhishek TYAGI wrote:
>> Dear Kenno,
>> Thanyou for your detail reply and instructions, actually I am alone doing
>> work on NAMD in my lab, even in my university, my Prof do not have
>> subsequent understanding of NAMD and even I don't have so any interaction to
>> Post doc/RA or other students, therefore, I directly ask you for the
>> problem. I have to do it myself and try to understand the things and do them
>> I hope in future you understand my situation.
>> From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of
>> Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu>
>> Sent: Monday, July 21, 2014 11:47 PM
>> To: namd-l_at_ks.uiuc.edu
>> Subject: Re: namd-l: Force field design
>> Dear Abhishek,
>> This list is full of very knowledgeable people who are very good at
>> resolving people's errors, but even the greatest guru cannot help you if
>> you don't tell them what exactly your problem is.
>> Since I get the impression you're relatively new to this, allow me to link
>> you to CHARMM's "parameter set discussion" forum guide lines:
>> I'm NOT suggesting you ask your question there. The CHARMM forums are for
>> CHARMM problems and the regulars don't like it if you post VMD/NAMD
>> problems. For NAMD, this mailinglist it the correct support channel.
>> Rather, the reason I'm giving you this link is that most of the good
>> practices it outlines are valid in *any* technical community, including
>> this list. In a nutshell, you are advised to search the web, consult the
>> valid resources (tutorials, FAQs...), experiment a bit yourself and
>> consult your advisor/mentor/senior postdoc before asking a question. Then,
>> if you must ask a question, take plenty of time formulating it, thinking
>> of it from the point of view of the expert trying to answer it. Make it
>> concise but include all relevant information.
>> Good luck,
>> On 07/19/2014 08:44 AM, Abhishek TYAGI wrote:
>>> Dear Kenno,
>>> Thankyou for the suggestion, I had read all the information provided so
>>> far and gone through the links in detail. But still I have a silly question,
>>> right now I have a.mol2 file and I got CGenFF a.str file, and for psfgen If
>>> I use a.str file it shows error, therefore I used CHARM-GUI to get psf and
>>> pdb file, I tried doe quick md on C-GUI it gives some topology and prm file,
>>> I used them for my simulation and got error, and for other files top and prm
>>> I still confused how to proceed.
>>> From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of
>>> Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu>
>>> Sent: Thursday, July 17, 2014 1:24 AM
>>> To: namd-l_at_ks.uiuc.edu
>>> Subject: Re: namd-l: Force field design
>>> On 07/15/2014 12:55 PM, Abhishek TYAGI wrote:
>>>> 1. I tried CGenFF and got a *.str file but the data in the file is
>>>> different from my input file i.e. mol2 file, the pdb format is different
>>>> from the *.str file.
>>> The str file contains a force field for your molecule, while the mol2 and
>>> pdb formats contain a geometry. How could the data not be different???
>>> The str file is a concatenated topology and parameter file. NAMD knows to
>>> ignore the topology section and can read the file as it is.
>>> I believe psfgen does the same (read the topology and ignore the
>>> parameters) though I'm less sure about that.
>>>> 2. I tried to get force field from swissparam website and received the
>>>> different file as *.par, *.top file, I tried MD on this field it runs
>>>> successful, but the question is that is this correct approach?
>>> It is strongly encouraged to search the archive before posting a
>>> If you had, you would have discovered the use of SwissParam for
>>> condensed-phase calculations is discouraged, and found advise on better
>>> ways to do it:
>>> Christopher Mayne's advice in this thread is sound.
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
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