recently, i use gromacs software, but i cannot calculate π-π staking by using this software.
thank you very much,my dear friend.
the following picture (figure 2e)is an example.
Did you try the GROMACS support (link below)?
http://www.gromacs.org/Support
dear friend, I have read this web, but found nothing.
Ger Koper,THANK YOU VERY MUCH!
good luck to you everyday!
Did you try one of the mailing lists?
thank you,Ger Koper, but I am not one of mailing lists.
Maybe you should subscribe to one?
Dear Wang
There is no way to compute π-π staking by using gromacs and the attached article used an external software (self programming) to count π-π staking.
27 February 2021 2,753 4 View
I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...
25 February 2021 6,314 1 View
Any technique could detect the degree of litter decomposed by microbes? Or any indexes could do this job? I want to split the contribution of microbes during decomposition, so any suggestions...
23 February 2021 1,362 5 View
To be specific, I want to conduct an IV regression in stata with the following three equations. EQ1: Y1 ~Y2 Y3 X EQ2: Y2 ~ Z1 EQ3: Y3 ~ Z2 Both Y2 and Y3 are endogenous. However, Z1 and Z2 are...
23 February 2021 6,266 3 View
The regenerated cellulose film was prepared by zinc chloride/H2O system. The zinc chloride had been washed away in the regeneration process, and the wet film which was not dried had uniform...
18 February 2021 9,538 1 View
Hi I've been looking for a stat package for my sensory evaluation data (progressive profiled which is a multi-timepoint version of descriptive analysis). Is there any available one to...
08 February 2021 9,170 3 View
Hi Everyone: I have a question regarding to qPCR. I am trying to do RT-PCR, and I want to have equal amount of input DNA for my RT-PCR, so I normalize my DNA input based on qPCR values of a...
31 January 2021 6,977 4 View
Hi Everyone: I want to quantify the relative amount of a protein in 2 samples. I will first digest the sample with trypsin, and subject the resulting peptides to LC-MS/MS analysis. I will then...
25 January 2021 8,333 3 View
Dear researchers, I am modeling the process of the water droplet impacting on the wall with a constant contact angle. The specific calculation parameters are as follows: The droplet diameter is...
24 January 2021 1,020 5 View
Does anyone have the similar issue? A line across the denature SDS gel shows up after staining with Coomassie blue and there are many lines in every lane if you take a closer look. This gel had 15...
07 January 2021 5,610 4 View
How to calculate the RMSD values for a MD simulation using MOE?
07 August 2021 0 0 View
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
effect of double bond on the flexibility of polymers
07 April 2021 0 0 View
I am writing to request some information for making polymer color flakes. I would appreciate the help.
17 March 2021 0 0 View
Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...
03 March 2021 8,796 3 View
I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance
03 March 2021 3,568 1 View