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Meetings & Events Jump to new posts
LCB Weekly Seminar 2021-2022 Ruben 01/25/22 07:10 PM
Laboratory of Computational Biology weekly seminar series

Meeting announcements for the weekly seminars hosted by the groups of Richard Pastor and Bernard Brooks (Laboratory of Computational Biology, NHLBI, NIH).


Laboratory of Computational Biology
National Heart, Lung and Blood Institute
12 South Drive, Bldg. 12A, Suite 3053
Bethesda, MD 20892-5690


Unless otherwise specified, seminars are currently at Thursday 12:00 noon by Zoom

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Date: Feb. 3, 2022
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Date: Feb. 10, 2022
Speaker: Dr. Thomas Dannenhoffer-Lafage
Affiliation: Robert Best's group, NIDDK, NIH
Presentation: TBA

Date: Feb. 17, 2022
Speaker: Dr. Cristina Fenollar Ferrer
Affiliation: NIDCD, NIH
Presentation: TBA

Date: Feb. 24, 2022
Speaker: Dr. Andreas Krämer
Affiliation: Frank Noé's group, Freie Universität Berlin
Presentation: TBA

Date: Mar. 3, 2022
Speaker: Dr. Aleksander Durumeric
Affiliation: Frank Noé's group, Freie Universität Berlin
Presentation: TBA

Date: Mar. 10, 2022
Speaker: Prof. Junmei Wang
Affiliation: School of Pharmacy, University of Pittsburgh
Presentation: TBA

Date: Mar. 17, 2022
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Date: Sept. 15, 2022
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0 29 Read More
Installation and Testing Jump to new posts
Re: Problem installing openmm on C46b1 (Free Version) rossi 01/16/22 02:48 PM
Dear Rick,

Thanks so much for your help and very quick response.

I will look at the information you provided.

Warm regards,

Angelo
16 420 Read More
Energy terms, Constraints, Restraints, and Solvation Jump to new posts
Energy inconsistency before/after SHAKE when using BLOCK ytao 01/15/22 03:46 AM
Hi there, I would like to ask a question about BLOCK module.

I'm using the BLOCK module in the CPU version of charmm (c47a1). I set up a three-block system and planned to run dynamics.
I was curious about the energy, therefore I called ENERgy before and after SHAKE (e.g. shake fast bonh param) before calling DYNA, then I found the two energies are different.

For example
before SHAKE:
ENER> 0-100167.71864 -7729.19789 6.88043
ENER INTERN> 4214.68967 3553.10667 271.98621 2030.41904 123.21122
ENER CROSS> -332.41288 0.00000 0.00000 0.00000
ENER EXTERN> 4828.07698 -86424.22023 0.00000 0.00000 0.00000
ENER IMAGES> 239.97592 -7390.48494 0.00000 0.00000 0.00000
ENER EWALD> 531.32747-505978.20960 484163.23345 0.00000 0.00000
ENER RESTR> 1.58238 0.00000 0.00000 0.00000 0.00000

after SHAKE:
ENER> 0 -95831.08338 -4336.63526 6.47747
ENER INTERN> 1079.16927 1598.97023 271.38280 2029.76266 122.77658
ENER CROSS> -332.77976 0.00000 0.00000 0.00000
ENER EXTERN> 4780.01659 -78725.23657 0.00000 0.00000 0.00000
ENER IMAGES> 231.78886 -6673.17411 0.00000 0.00000 0.00000
ENER EWALD> 548.58184-505978.20960 485214.28512 0.00000 0.00000
ENER RESTR> 1.58271 0.00000 0.00000 0.00000 0.00000

I also checked other systems without using BLOCK module, and two energies are consistent.
In addition, if I use "ENERgy omm", the two energies are almost identical.

Please feel free to advise. Thanks.

YT
0 61 Read More
QM/MM Discussion and Questions Jump to new posts
Re: QChem input file generated by CHARMM in QM/MM Alpha 01/13/22 05:22 PM
Thank you Lennart!
2 107 Read More
QM/MM Discussion and Questions Jump to new posts
Adding more than 1 link atom in QM/MM Alpha 01/12/22 07:23 AM
Greetings,

I am trying to do a QM/MM calculation, using CHARMM and Q-Chem, following the steps in the tutorial by Prof. Kaila https://villekaila.com/news/

When I add a hydrogen link atom to cap a cut C-C bond, using addlinkatom, it works fine. However when I add two links atoms, I get the following error:

"No parameter for QM-link atom"
Adding each of the two link atoms alone works fine, the parameters are found. But when I add both, it looks like only the parameters of the first link atom are detected, but not the second one.

Any suggestions as to how I can fix this?
Thank you in advance,
Regards,
Alpha
0 65 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: Residue Name for C-terminated Amide in GROMACS PDB Input tim0marshall 01/05/22 04:56 PM
Thank you.

I read the March 2016 edited version, but failed to figure out the appropriate place for the post. Sorry about that.
2 84 Read More
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