Hi,
I am working with NAMD but I need to know about gmx genrestr and isometric force constant. What that it mean? Is it like pulling and Steered molecular dynamics (SMD) in NAMD?
Thank you in advance
Dear All, I wonder what is the best choice for saving and storing trajectory files (dcd and ...) and all other sensitive and delicate items? any special brand of external hards? regards
02 March 2019 6,503 1 View
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01 February 2019 7,781 1 View
Hi all, I am trying to simulate a protein containing a modified Lysin : Trimethyllysine. I am a NAMD user and I couldn't find a proper forcefield (topology and parameter files) with charmm yet....
11 December 2018 7,202 9 View
these two algorithms seems fast and efficient for aligning (superpose) two proteins: Acta Chrystallogr. Sect. A 61 (2005) 478 [doi: 10.1107/S0108767305015266] J. Comput. Chem. 31 (2010)...
08 September 2018 9,510 1 View
Hi, I need help with performing a simulation of a ligand and a protein. I am using psfgen code and add a ligand as the second segment but my parameter file couldnt recognize the new molecule...
08 September 2018 9,632 6 View
Dear All, According to VMD, two plug-in called Autoionize and Cionize are able to neutralize a normal system and highly charged system,respectively. In Gromacs we have only genion for both. Can...
06 July 2018 6,728 0 View
Hi everyone. I am new in the field of molecular dynamic. Would you please help me with altering large DCDs? I want to extract the C-alpha trajectory from my large dcd which is too large to be...
11 December 2017 7,946 6 View
How to calculate the RMSD values for a MD simulation using MOE?
07 August 2021 0 0 View
When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.
16 June 2021 0 0 View
Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...
03 March 2021 9,989 2 View
Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...
03 March 2021 5,978 5 View
Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...
02 March 2021 2,431 3 View
Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...
02 March 2021 4,910 3 View