Can anyone help me with my problems pulling a molecule across the lipid bilayer in a steered MD simulation in GROMACS?

I am using following pull code in the steered md simulation in gromacs for pulling a molecule across the plasma membrane model. ; Pull codepull = umbrellapull_geometry = distancepull_dim = N N...

03 April 2015 187 6 View

Pressure and density values not converging to reference values in membrane simulation in gromacs 5.0.4 ?

I am trying to simulate the membrane patch of 5 lipid mixture obtained from the CHARMM-GUI (I edited the output README file as 1 to 20 for getting a total of 20 ns production run, and all...

02 March 2015 8,651 3 View

GRID computing, how to setup a grid computing over the local area network, in case of molecular dynamic software (is it possible with gromacs or NAMD?

GRID computing, how to setup a grid computing over the local area network (LAN). In case of molecular dynamic software, is it possible with gromacs or NAMD to use grid computing to increase the...

01 February 2015 6,271 3 View

On which basis I should choose the lipid type for PC, PE etc, if I need to model the human Macrophage membrane?

On which basis I will choose the lipid type for PC, PE etc, if I need to model the human Macrophage membrane among (because chain length of fatty acid and fluidity of the membrane will vary with...

01 February 2015 3,843 1 View

In CHARMM-GUI online server .mdp output file for equilibrium and production run has no pbc condition defined?

In CHARMM-GUI online server .mdp output file for equilibrium and production run has no pbc condition defined by default. So here I have to add pbc condition manually to all .mdp file, or no need...

01 February 2015 5,144 3 View

Fatal error: Group pull_group1 required by grompp was undefined?

I followed tutorial exactly same as mentioned on http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html for umbrella sampling but following command produced...

01 February 2015 4,455 4 View

How do I solve this error and how I can install gromacs through yum?

Getting error during gromacs 5.0.4 installation on centOS 6.6 -- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2Downloading:...

31 December 2014 283 9 View

Can anyone suggest me how to do/check the effect of variable ph range (acid expansion) on the protein structure by Gromacs MD simulation?

As we know that there is acid expansion of protein when we change the native ph of the protein. I want to prepare a protein at ph 4.7 (protonation state, as assay system was set to 4.7 ph) which...

10 November 2014 4,071 7 View

Do you think that MTH1 inhibitors can be a break-through in cancer treatment without any, minimal or acceptable side-effects?

Do you think that MTH1 inhibitors can be a break-through in cancer treatment without any, minimal or acceptable side-effects?

10 November 2014 2,411 4 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 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

MD MOE RMSD

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

07 August 2021 0 0 View

MGL tools

20 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

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

i have some problem with chtMultiRegionSimpleFoam

--> FOAM FATAL ERROR: Maximum number of iterations exceeded From function Foam::scalar Foam::species::thermo::T(Foam::scalar, Foam::scalar, Foam::scalar, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar) const) const [with Thermo = Foam::hConstThermo >; Type = Foam::sensibleEnthalpy; Foam::scalar = double; Foam::species::thermo = Foam::species::thermo >, Foam::sensibleEnthalpy>] in file /home/ubuntu/OpenFOAM/OpenFOAM-4.1/src/thermophysicalModels/specie/lnInclude/thermoI.H at line 66. FOAM aborting #0 Foam::error::printStack(Foam::Ostream&) at ??:? #1 Foam::error::abort() at ??:? #2 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::calculate() at ??:? #3 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::correct() at ??:? #4 ? at ??:? #5 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #6 ? at ??:?

24 March 2021 0 0 View