How good to use triclinic box for gormacs simulations?

I have performed simulations for Protein RNA complex around 1500 residues. I have used triclinic box with 1.4 nm distance from the edge of the box to protein as triclinic box takes less number...

09 October 2017 1,429 1 View

How to consider protonation states of histidine in Gromacs simulation?

08 September 2017 223 1 View

How can I utilize all the CPUs in one node during gromacs simulations?

I have installed gromacs 5.1 in server which has 4 nodes each with 40 CPUs. I am allotted to use only 2 nodes with 80 CPUs. after installation when i did sample md run only 20 cpus are being...

08 September 2017 9,639 3 View

Any suggestions on generating ligand toplogy using OPLS all atomic force field compatabile to gromacs?

I am currently working on drug complex, i am using OPLS-AA force field, i have to generate a topology file for ligand compatible to gromacs using OPLS-AA. any suggestions please... Thanks in advance

05 June 2015 5,768 2 View

How do you replicate the number of lipids in bilayer for membrane dynamics using gromacs?

03 April 2015 8,994 5 View

How can I rename the lipid.itp file in order to match gromos53a6.ff for membrane dynamics using gromacs?

03 April 2015 5,217 3 View

Using 20 frames (each 5ns ) from 100ns are reliable to calculate binding free energy calculations?

I wanted to calculate binding free energy calculation of my complex (protein +inhibitor). I have no resources to calculate for large number of frames (ie, 5000 frames from 100ns) hence I have...

09 October 2014 3,536 10 View

PCA and NMA approaches on MD simulation trajectory is same?

I have done 100ns simulations for my protein using gromacs, and then subjected to PCA analysis from gromacs (g_cova, g_anaeig). In order to see the dominant motion within the proteins (WT and...

05 June 2014 5,544 4 View

How reliable is the average structure of trajectory from gromacs simulation

While taking the average structure from GROMACS simulations of a complex, which average structure is reliable? For example in GROMACS there are three options ox (average), oq(bfactor) and...

05 June 2014 7,990 1 View

What are your suggestions on my unphosphorylation approach?

In order to construct unphosporylate kinase, I have replaced phopothreonine with threonine from active crystal structure computationally, as there is no inactive crystal coordinates for my kinase....

04 May 2014 5,924 0 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

Can linear DNA be used as template for site-directed mutagenesis?

Is it possible to induce site-directed substitution mutation by quick-change method on linear dsDNA? or it has to be cloned in some vector? If yes, should it be treated with the Dpn1 enzyme...

03 March 2021 401 4 View

What solvent can I used for Paal Knorr reaction between 6-amino hexanoic acid and 2.5 hexanedione?

I am try to make the Paal Knorr reaction between 2.5 hexnedione and 6-amino hexanoic acid, my problem is type of solvent to use, because 6-hexaminohexanoic acid is soluble in water but I am not...

02 March 2021 4,443 2 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