Re: Force field design

From: Gianluca Interlandi (
Date: Wed Jul 23 2014 - 23:30:58 CDT

Just to add my 2 cents to the conversation. PIs who wish to bring the MD
expertise into their lab should consider hiring a postdoc or research
scientist with the necessary skills and knowledge. I'm sure there is a
number of potential postdocs out there with a solid training in MD who
would be willing to join a mainly experimental lab. There is the question
of funding, but there are also postdoctoral fellowships.


On Wed, 23 Jul 2014, Kenno Vanommeslaeghe wrote:

> I think Axel is right; you really need to talk with your PI about spending a
> few months in an MD lab. Universities and granting agencies commonly have
> funds for a grad student to do so, so he has everything to win and nothing to
> lose. And that goes double for you.
> As for your complaint about perceived lack of online resources, to continue
> with the analogy from my posts on the CHARMM forums (do read them), if you
> buy an NMR or X-ray crystallography machine, the vendor will provide you with
> manuals and training to allow you to use the machine at a *technical* level.
> However, this alone will *not* allow you to use the machine to solve
> scientific problems. For that, you also need:
> - scientific background
> - the know-how to combine you scientific background and technical skills into
> effective research and valid/relevant results
> Scientific background you can get from university courses and textbooks, but
> there's no way to obtain know-how but to learn it form a more senior
> researcher. No vendor in the world provides training for *that*. Also, you
> don't seem to realize we are not vendors; we are academics. Our main priority
> is to publish, and even though you may not experience it as such, we're only
> helping the community out of kindness. But, we cannot help the "many users
> like you", especially not over e-mail; that's like trying to empty an ocean
> with a teaspoon (while it's raining). We're mainly here to help the people
> who have gone through the effort of acquiring know-how solve nontrivial
> problems that are poorly documented or not common knowledge in the community.
> On 07/23/2014 01:23 AM, Abhishek TYAGI wrote:
>> Dear Axel,
>> Thankyou for your elaborated email reply, I am agree few of the points but
>> not all, their are many users like me using NAMD and try to learn it by
>> online resources available, and I think most of them face these problems
>> during their work that I am facing right now. I have to all the things
>> myself I appreciate your way of explaining each and every point in detail,
>> this will help me to plan my work in future.
>> regards
>> Abhishek
>> ________________________________________
>> From: Axel Kohlmeyer <>
>> Sent: Wednesday, July 23, 2014 12:36 PM
>> To: Abhishek TYAGI
>> Cc:
>> Subject: Re: namd-l: Force field design
>> On Wed, Jul 23, 2014 at 12:04 AM, Abhishek TYAGI
>> <> wrote:
>>> Dear Axel,
>>> 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.
>> so attend lectures, attend tutorials, invite people to come visit and
>> teach you or go spend some time at a group that has the necessary
>> expertise. if you are willing you have to be willing to learn things
>> *the right way*. at the moment, you are *not* doing this. remember
>> that with great power comes great responsibility.
>>> 2. If you demotivate everyone like this than in future the NAMD user
>>> number will be effected.
>> so what? this is not a competition about how many users a software
>> has. that is a stupid way of seeing things. it is not then number of
>> users that matters, but the number publications that are done
>> correctly and properly.
>> if you read my mail correctly, you should have seen that i do not want
>> to demotivate you, but rather do the opposite. go to your adviser and
>> stand up for your needs. insisting to do something without knowing
>> what you are doing and without the proper training using an
>> inefficient communication medium (e-mail) is something that you do to
>> yourself and if that is demotivating and frustrating for you, then
>> this is *your* fault, not anybody else's.
>>> 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.
>> no. this is a ridiculous demand. please read the link that kenno
>> provided. on top of that, your problems are not at all NAMD specific
>> problems, but general MD problems and it is *not* the task of NAMD
>> developers to provide the information and training how to do MD in
>> general. why not demand this training from the charmm folks, or the
>> amber folks, or the gromacs folks or the materials studio folks or the
>> macromodel folks or anybody else that provides an MD code.
>>> 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.
>> this is the job of your adviser not mine. your adviser gets paid for
>> it and i am not.
>>> regards
>>> Abhishek
>>> ________________________________________
>>> From: <> on behalf of
>>> Axel Kohlmeyer <>
>>> Sent: Wednesday, July 23, 2014 12:14 AM
>>> To: Kenno Vanommeslaeghe
>>> Cc:
>>> Subject: Re: namd-l: Force field design
>>> On Tue, Jul 22, 2014 at 11:40 AM, Kenno Vanommeslaeghe
>>> <> wrote:
>>>> 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
>>> misinterpreted.
>>> axel.
>>>> 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.
>>>> Cheers,
>>>> Kenno.
>>>> 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.
>>>>> regards
>>>>> Abhishek
>>>>> ________________________________________
>>>>> From: <> on behalf of
>>>>> Kenno Vanommeslaeghe <>
>>>>> Sent: Monday, July 21, 2014 11:47 PM
>>>>> To:
>>>>> 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,
>>>>> Kenno.
>>>>> 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.
>>>>>> regards
>>>>>> Abhi
>>>>>> ________________________________________
>>>>>> From: <> on behalf of
>>>>>> Kenno Vanommeslaeghe <>
>>>>>> Sent: Thursday, July 17, 2014 1:24 AM
>>>>>> To:
>>>>>> 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.
>>> --
>>> Dr. Axel Kohlmeyer
>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> International Centre for Theoretical Physics, Trieste. Italy.
>> --
>> Dr. Axel Kohlmeyer
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.

Gianluca Interlandi, PhD
                     +1 (206) 685 4435

Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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