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

CCSD(T) calculation of Open shell singlet cation ?

I would like to calculate the energetics for open shell singlet Sc+ and Sc+(OH2) using CCSD(T) level. As if we consider default Gaussian procedure, it seems to be considered close shell singlet....

11 December 2018 8,894 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

Could you recommend any books about Number Theory?

Beginner level books. High level books. Analytical Number Theory. Algebraic Number Theory. Combinatorical Number Theory. Books about partitions. Books about primes.

03 March 2021 7,174 5 View

Can we classify HV and LV lines based on line length?

I have dataset which shows the length of power lines. I need to classify the lines based on the line length. Is there a rule to classify the High voltage (HV) and low voltage (LV) lines based on...

03 March 2021 4,116 4 View