Why does npt equilibration generate free space ?

During the nvt it was okay. After the NVT equilibration, short NPT equilibration was performed. During this equilibration, free space generated inside box. Please tell me some possible reasons?

09 October 2018 8,546 0 View

How to estimate hydrophobic interactions and electrostatic interactions between the protein chains using GROMACS?

Dear GMX experts, A simulation system consists of several peptide chains, and I would like to compare contacts of hydrophobic and electrostatic interaction. How can I estimate hydrophobic...

03 April 2018 9,735 3 View

How to convert CHARMM .str to .itp file for GROMACS?

Dear Experts, I generated LIG.str file using CGenFF for a specific molecule. I would like to use GROMACS package. I tried to convert LIG.str file to LIG.itp file. I tried as following command...

31 December 2017 9,258 3 View

How can I know the structure was optimized or not?

Hello, I am very new user of Gaussian. I started the optimization of the connected two amino acids. Calculation was finished, and I would like to get the optimized structure. How can I know...

05 June 2017 7,037 5 View

Can someone verify my singular value decomposition of 3D helical data?

01 February 2016 8,378 0 View

How do I make a pH dependent simulation of Oligomer structures?

Hello, I want to make pH dependent simulation of dimer, trimer and pentamer structure of peptide. How to make it using AMBER or GROMACS? Can I use H++ server for oligomers? or How to set manually....

31 December 2015 769 2 View

How to fix malloc error during MM-PBSA calculation on AMBER14

Hello, I have got following error during MMPBSA.py calculation for PBSA MD simulation. How to fix it? ******************************************************************** Beginning GB calculations...

10 November 2015 10,029 2 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