Does gromac 5.0.2 has seperate gpu to be compiled?

More Seshank Mutya's questions See All

How to write covar.ndx?

I want to test dihedral PCA for my mutated pocket and have trouble understanding the tutorial. How can i generate covar.ndx from the dihedral angles generated in before step. And regarding the...

03 April 2016 9,876 2 View

Mutation causing integer unperturbed charge of system. What to do?

The wild type protein has shown no integer charge where as a mutation in protein R175H has produced an integer charge in system. I used pymol to mutate. is it the centre of problem. Help wil be...

03 April 2016 4,356 2 View

How to renumber residue numbers in .gro and .top?

how can i renumber .gro and .top residue numbers to start with a specific number. The scenario is that i have first 40 residues of DNA and i dont want to disturb them. I just want to renumber from...

02 March 2016 477 1 View

How to perform cationic dummy atom model for a zinc contaning protein?

I am finding it difficult to perform cationic dummy atom model for p53 protein. can anyone suggest me a good and little detailed procedure. * if i perform it with xleap program of ambertools14,...

01 February 2016 2,946 0 View

[SOLVED]How to solve xleap error ( no leaprc in search path)?

I am getting an error in xleap module of Ambertools 14 in which it is unable to find leaprc nor anyother file i added to respective folders as said in this tutorial...

01 February 2016 7,368 2 View

How to get minimum energy structure from MD?

how can we decide on least energy structure of protein and ligand complex from MD simulation.

01 February 2016 5,285 1 View

Can youSuggest me best softwares for TEMPLATE DOCKING of ligands?

Molegro Virtual Docker is now little difficult to access and use so can any one please suggest better reliable software for template based LIGAND docking where a template of the ligand is made and...

09 October 2015 9,015 0 View

Why is measurefit in VMD showing following error "measure fit: selections must have the same number of atoms" ?

I tried to align molecules basically proteins at different frames to understand the ligand interaction. But to my dismay it shows an error "measure fit: selections must have the same number of...

08 September 2015 8,589 0 View

Is there a way to decrease gpu/cpu ratio of performance in GROMACS?

when ever i run a simulation in gromacs i end having a note saying GPU is 20% more in use than cpu which could decrease the performance and GPU/CPU ratio is 7.5 which should be ideally. Suggest me...

07 August 2015 2,557 0 View

How can I improve the GA341 score in the modelled protein in modeller?

I have performed series of modelling experiments using modeller to get a series of modeller proteins. But here i am unable to produce models with good GA341 score. I have a hundred percent match...

02 March 2015 6,043 9 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

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

Dear all, I was wondering if anyone knows whether MGLtools and Autodock can run on Mac OS?

I have tried to download the 64-bit version of MGLtools however, as many times as I have downloaded and uninstall the programs, an error arises that the app needs to be updated. Thank you.

03 March 2021 5,997 2 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 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

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

Justin Lemkul

GPU support is enabled if the required CUDA libraries, etc. are found during installation. If they are not found, GPU support is disabled. You also need a supported GPU, which by default MacBook Pros do not have.

Seshank Mutya

what can be done if i have a macbook pro and want a gpu acceleration for GROMACS. Could you please suggest a way.

i have a GE force graphic processor installed

http://www.gromacs.org/Documentation/Installation_Instructions_5.0#native-gpu-acceleration