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 a way out to improve my performance.
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 4,422 2 View
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 9,970 2 View
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 571 1 View
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 3,082 0 View
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 7,648 2 View
how can we decide on least energy structure of protein and ligand complex from MD simulation.
01 February 2016 5,370 1 View
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 9,093 0 View
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 8,854 0 View
i am a newbie to gromacs(molecular dynamics software), please help me out. i compiled gromacs 5.0.2 for mac and successfully done installing it. But when i checked the following command mdrun...
05 June 2015 2,670 4 View
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 6,188 9 View
Can anyone explain this method? Especially the last statement where it says only at 1.5 to 2.5mins was the MS/MS connected to the UPLC. How is that possible, is it a feature in this specific...
11 August 2024 8,141 3 View
I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...
07 August 2024 2,598 1 View
Hello What should be done to separate and identify organic acids in HPC when their RetTime is the same?Like oxalic acid with Propanoic Acid.or acids that have a very close RetTime.
07 August 2024 8,782 3 View
Dear QE-users, In the method where full MS positive mode and PRM mode are used, we always get an incorrect auxiliary gas reading (41 instead of 25). This only happens in this method; other...
06 August 2024 4,953 0 View
Mobile apps can be a powerful tool for enhancing academic performance, how can we use mobile apps for improving academic performance
04 August 2024 9,492 0 View
Hello guys! Do you have experience running a Oaxaca-Blinder decomposition on R applying person weights. How do you suggest doing it? I have a variable PERWT which gives more information on how...
04 August 2024 6,033 0 View
Hi everyone, I'd like to better separate two close peaks coming from a bioconversion sample, I'm currently using a C18 KromaPhase 4,6mm Ø.I. SCHARLAU, particle size (µm): 10, pore size (Å): 100,...
30 July 2024 435 3 View
Hello Everyone I have a question about structure for connectivity analysis on sources. My goal: preprocess and cut data into trials create headmodels, using template MRI file perform source...
30 July 2024 2,744 1 View
When I run autogrid4 it says: autogrid4: ERROR: Unknown receptor type: "Cr" -- Add parameters for it to the parameter library first! Look forward to your reply.Thank you so much!
29 July 2024 488 0 View
I am trying to run a restart analysis, which imports deformed configurations of parts from a generated ODB file. It runs fine in Windows OS but when I try to run it in Linux OS, it is giving some...
29 July 2024 9,572 3 View