Why partial charge on chlorine atom from GAFF is +ve?

I am looking for an Amber based force field for chloroform as solvent to use with Gromacs. I adopted GAFF ff from http://virtualchemistry.org. The partial charge on chlorine and carbon which are...

07 August 2019 8,352 4 View

Which thermostat and pressure couple are preferred for MD and why?

I have simulated my system with two thermostat, Noose-hoover and V-rescale, with same pressure couple. I got slightly different results for the two different thermostat. What could be the possible...

05 June 2018 4,102 2 View

Gromacs PBC: What the difference when I put periodic-molecules "yes" or "no" with pbc in all xyz direction?

I checked it in the manual which says if periodic-molecules is set to no, "molecules are finite, fast molecular PBC can be used" and if it is set to yes " for systems with molecules that couple...

03 April 2018 4,426 0 View

DNA-Protein complex simulation with GROMACS using Charmm36 Force field.

I have simulated a DNA-Protein Complex structure with 150mM NACL salt concentration for 100 nanoseconds. The simulation is completed with not much problem, but while visual analysis in VMD of the...

04 May 2017 7,947 10 View

How to incorporate NMR Chemical Shift data as restraint in MD for protein-ligand complex?

01 February 2017 1,830 2 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

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

fatal error

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

fatal error

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

fatal error

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

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

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

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

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

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

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

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View