VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Mon Nov 07 2022 - 22:49:33 CST

Please keep the list copied in replies.

I went through the tutorial, generated the files, ran the simulation, and clearly see what’s expected. I then ran the simulation with your files and again, I see what I expect. I can only think of a couple possible things: 1) there’s a difference in our mdff_template.namd files (shouldn’t be but you didn’t have this in the files you provided) or 2) something is wonky with the version of NAMD you used (NAMD 2.14 for Win64-multicore-CUDA). Can you try with a different version of NAMD and see? It would be good to know if one of them has a bug.

Best,
JC

On Nov 7, 2022, at 12:08 AM, Stefan Lyne Oliver <sloliver_at_stanford.edu<mailto:sloliver_at_stanford.edu>> wrote:

Thanks for the reply, JC. Here’s a link to a shared folder that contains all of the files that were generated following the tutorial instructions…

https://urldefense.com/v3/__https://drive.google.com/drive/folders/1lb6rMaxNPQJLiOXg21oZPNqDaYIn3DLR?usp=sharing__;!!DZ3fjg!4-347YaJgeEY8KxGavMl-vhFsdJ89GOs0TEMJpv3ESheyUBtcCYInpQv3n2XauBU1Zuxyjwn84r68RyFcYHE3ynPEyI$

There are also two subfolders for the NAMD-step1 and -step2 outputs.

Many thanks!

Stefan

From: Gumbart, JC <gumbart_at_physics.gatech.edu<mailto:gumbart_at_physics.gatech.edu>>
Sent: Sunday, November 6, 2022 13:29
To: Stefan Lyne Oliver <sloliver_at_stanford.edu<mailto:sloliver_at_stanford.edu>>
Cc: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: RE: Simple MDFF Tutorial - 1ake does not fit into map

Can you provide your files somewhere so others can take a look?

Best,
JC

On Nov 4, 2022, at 7:52 PM, Stefan Lyne Oliver <sloliver_at_stanford.edu<mailto:sloliver_at_stanford.edu>> wrote:

Hi All,

I’ve still not come up with a solution for the problem below. Is there anyone who can advise?

Cheers,

Stefan

From: Stefan Lyne Oliver
Sent: Tuesday, 1 November, 2022 20:10
To: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
Subject: Simple MDFF Tutorial - 1ake does not fit into map

Hi All,

I’ve been working through the simple MDFF tutorial. Unfortunately, after completing the NAMD (2.14 for Win64-multicore-CUDA) simulations the 1ake does not fit into the map. There is evidence that the molecular dynamics is working as I can see movement of the 1ake model after I’ve performed the NAMD simulation. I’ve tried this on two different windows machines (VMD 1.9.4a53) with reproducible results. The provided ake-step1-result.dcd and ake-step2-result.dcd files work fine when I load the molecules so I must be missing something in the tutorial. I’ve spent a fair amount of time on this and also discovered what seem to be some errors in the commands e.g. it looks like in the ‘Defining secondary structure restraints’ section the 1ake-initial_autopsf.psf file in step 2 should be 1ake-initial-docked_autopsf.psf. Correcting either way produces the same results. Can you please let me know what I’m missing in the tutorial so that I can be confident in using the procedure on my own maps and models. Thanks in advance.

Best wishes,

Stefan

Stefan Oliver, Ph.D.<https://urldefense.com/v3/__https:/profiles.stanford.edu/stefan-oliver__;!!DZ3fjg!-RcSuTdw9bWJ9ej-TyzBAd_siy68pglqwMic7u6tDtImmwMF1gfZK3oaJ24pWJk_r1btyGFzHIzORB9Rf7a6a5U$>
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E-mail: sloliver_at_stanford.edu<mailto:sloliver_at_stanford.edu>
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