Missing pulling information while performing Steered Molecular Dynamics ?

Dear all, This is regarding the Steered Molecular Dynamics. After finishing SMD, extracted useful frames from the SMD trajectory and performed the brief NPT equilibration of the selected useful...

11 December 2019 6,756 2 View

Is there any other way to calculate the surface area per lipid of 200 ns trajectory, other than using MEMPLUGIN of VMD?

Hi Everyone, I am calculating the surface area per lipid of 200 ns membrane trajectory using MEMPLUGIN of VMD and it seems to be calculating the same too slow. Therefore, I would like to ask Is...

05 June 2019 3,350 4 View

Calculate Radial Distribution Function using ONIOM gaussian results

06 July 2017 1,230 0 View

How can one continue the MD simulation in Gromacs if simulation has terminated, but not completed?

I am running the MD simulations for 30 ns which is 15000000 nsteps using dt= 0.02 using GROMACS software but it has terminated (after 13000000 steps) before completion due to queue limits. I would...

05 June 2017 7,307 10 View

Can anyone suggest me what type of atoms of phospholipid headgroup have to select for lipid headgroups density analysis?

05 June 2017 1,953 1 View

How can I get torsion potential?

11 December 2016 6,490 13 View

How do we calculate -center x y z (Coordinates of geometrical center), when we orient the protein in bilayer membrane?

I need to construct a mixed lipid bilayer for simulating a membrane protein. I am trying in GROMACS, but I have a problem in orientation of protein in lipid mixed type lipid bilayer.

05 June 2015 3,613 4 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

flexibility of polymers chain

effect of double bond on the flexibility of polymers

07 April 2021 0 0 View

Formulation of polymer color flakes

I am writing to request some information for making polymer color flakes. I would appreciate the help.

17 March 2021 0 0 View

I am interested in medicinal chemistry field, which books are highly recommended to learn from?

I am at the beginner level in drug design and drug discovery, and I am interested to learn more about this field. Which books are highly recommended to start from and gives me all essential...

02 March 2021 8,437 2 View

How Relativistic effects is one reason for lanthanide contraction?

The Lanthanide contraction which is the decrease in ionic radii of the elements in the lanthanide series from atomic number 57, lanthanum, to 71, lutetium, is due to poor shielding of the 4f...

01 March 2021 2,272 4 View