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Dear All, I wonder what is the best choice for saving and storing trajectory files (dcd and ...) and all other sensitive and delicate items? any special brand of external hards? regards
02 March 2019 6,601 1 View
Hi all, I am trying to simulate a protein containing a modified Lysin : Trimethyllysine. I am a NAMD user and I couldn't find a proper forcefield (topology and parameter files) with charmm yet....
11 December 2018 7,292 9 View
Hi, I am working with NAMD but I need to know about gmx genrestr and isometric force constant. What that it mean? Is it like pulling and Steered molecular dynamics (SMD) in NAMD? Thank you in advance
09 October 2018 9,291 0 View
these two algorithms seems fast and efficient for aligning (superpose) two proteins: Acta Chrystallogr. Sect. A 61 (2005) 478 [doi: 10.1107/S0108767305015266] J. Comput. Chem. 31 (2010)...
08 September 2018 9,618 1 View
Hi, I need help with performing a simulation of a ligand and a protein. I am using psfgen code and add a ligand as the second segment but my parameter file couldnt recognize the new molecule...
08 September 2018 9,725 6 View
Dear All, According to VMD, two plug-in called Autoionize and Cionize are able to neutralize a normal system and highly charged system,respectively. In Gromacs we have only genion for both. Can...
06 July 2018 6,849 0 View
Hi everyone. I am new in the field of molecular dynamic. Would you please help me with altering large DCDs? I want to extract the C-alpha trajectory from my large dcd which is too large to be...
11 December 2017 8,084 6 View
The paper in question is "Interpolation of Nitrogen Fertilizer Use in Canada from Fertilizer Use Surveys". This paper was very recently published by Agronomy (MDPI). Agronomy has, in the last day...
07 August 2024 9,934 3 View
Program: g_mmpbsa, version 2024.1 Source file: extrn_apbs.cxx (line 152) Fatal error: Failed to execute command: $APBS pybYcUWA.in --output-file=pybYcUW.out
07 August 2024 6,066 0 View
The first pdf file I uploaded had an error. So I uploaded an updated, corrected pdf of that paper with a different pdf name. I dpon't want the old copy to be download or read.
07 August 2024 9,508 1 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
Dear Researchers Kindly share JCPDS 65-7246 file Thanks in advance
04 August 2024 5,613 1 View
Hi everyone I need a file with a dirty and clean potato image
04 August 2024 7,199 4 View
I am conducting my analysis using SPSS. I log transformed my data using In(X+1) as my data contain zero values. However, when I want to back transform the regression coefficients generated from my...
31 July 2024 7,860 3 View
How to change the displayed full article text to its corrected version? In the file on the page of the journal where I published the article, there was an error in the text, the table is...
30 July 2024 3,229 2 View
Difficulty with permittivitt and Magnetic Permeability Calculations Hello everyone, I have all the parameters related to the calculations of the permittivitty and magnetic permeability...
30 July 2024 5,206 1 View
i m interested in pca analysis of c-alpha atoms in gromacs for that i used the following gmx_mpi covar -s mdca.tpr -f mdca.xtc -o eigenvalca.xvg -v eigenvecca.trr -av average.pdb -n index.ndx but...
30 July 2024 1,607 1 View
