From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Tue Jul 22 2014 - 10:40:37 CDT
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 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
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 carefully.
> 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 question.
>> 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.
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