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Questions related to Computational Chemistry
Dear all, I got confused. I have optimized the geometry and calculated the SPE also on the optimized geometry. I think it's right (correct me if I'm wrong. I'm beginner). I saw one paper in...
12 January 2016 9,845 6 View
Hi all, I have a problem with my simulations which I have performed through gromacs. Same error appeared in all simulations . VMD figure of final complex after simulation is attached. I think it...
12 January 2016 5,515 11 View
I have the latest version of avogadro but it can't do all the things that are shown in the youtube videos, for example, under >extension>surface type, I have only vanderwaals and...
08 January 2016 276 3 View
I am a complete beginner to computational chemistry but have recently started using ORCA to calculate vibrational spectra of various long side chain glycolamides. However, these molecules can have...
06 January 2016 8,412 10 View
I want to calculate the d-band center of Pt(111) surface. I am using the VTST script of Henkelman's group. Can anyone tell me how to use the dosanlaze.pl using LORBIT=11. Supppose, I have 5 atoms...
25 December 2015 4,965 1 View
Probably, there is some server error in DUDE-E decoy generation. As it keeps on sending empty files whenerver i had submitted by ligands for decoys generation. Can anybody tell me some alternate...
22 December 2015 8,213 5 View
Dear all, I was trying to calculate the Hammett constant of some special groups (no experiment data). while the reviewer told me it could be done by software. what he/she said was 'approach...
18 December 2015 4,885 3 View
Dear, Actually I am performing a sp CCSD(T)/aug-cc-pvQz (in gaussian09) with around 720 basis functions and 1100 primitive gaussian of size (the compound has pseudo-potential core for a metal) on...
07 December 2015 4,943 9 View
Does anyone have Gaussian script with RECP basis set?
04 December 2015 7,978 2 View
hi, in a structure based virtual screening, i have used zinc database for docking ligands with schrodinger maestro glide. after docking xp, I have perform a mmgbsa. how i can extract best 10...
02 December 2015 7,198 5 View
Hi everybody. I'm looking for GPU-accelerated packages in DFT calculations, I wonder if anyone knows an accurate package which also supports GPU acceleration (except quantum-espresso), and how...
02 December 2015 3,904 4 View
I am performing QM/MM using Qunapol. The default steps of quanpol optimization is 10000 but i want to perform the optimization for 100 ps with 1 time step = 1fs, therfore, i have increased the...
01 December 2015 4,169 3 View
I am trying to simulate water by using AIMD simulation with VASP. The LDA is used and about 70 water molecules are placed in a box. The following parameters are my setting in INCAR. However, the...
25 November 2015 5,132 6 View
Hi all, For a while now I have been building a small application to generate AMBER forcefield compatible force constants (stretch and angle). I use the full Force Constant matrix for a Gaussian...
22 November 2015 7,304 15 View
We investigate a dimer of an organic molecule. It is linked together by two hydrogen bridges. a) What is the best way to calculate the bonding energy of the dimer? One possible approach is...
22 November 2015 9,093 11 View
design of experiment in chemistry is important and caused saving time and material. many software like spss, mini tab, Design expert 9 and etc used for this Purposes
18 November 2015 3,753 65 View
Hello, I'm using Gaussian 09 to try and calculate the adiabatic electron affinity (AEA) of H3PO4. I've done this by running a geometry optimizations and frequency calculations of both H3PO4...
08 November 2015 8,946 3 View
I am optimizing some structures at the doublet potential energy surface. I know that the eigenvalue of operator S2 should be near to 0.75 on the doublet potential energy surface...
07 November 2015 2,462 6 View
Dear all I have to calculate SPEs for some (25-30 molecules of max 15 atoms of 60-65 electrons in one molecule) molecules and applied CCSD(T)/6-311+g(3df, 2p) theory to do that but it is taking a...
06 November 2015 7,329 7 View
From what I read so far, I see that there are some heme a/a3 force filed parameters for both reduced and oxidized state of heme. Is there similar kind of parameters and also topology files to be...
02 November 2015 3,375 5 View
Hello to everyone, I am working on the modeling of a class of FMN-dependent NAD(P)H enzymes, where FMN is tightly bound to the protein. Interaction Fingerprints (IF) seems to be a powerfull tool...
27 October 2015 8,460 1 View
I have performed MD simulation of protein-peptide complex for 300ns time interval using GROMACS-5.0.4 on cluster and write frames at every1ns. I ran the simulation in triplicates. When I was...
27 October 2015 2,592 4 View
I am reconstructing the force constants from the weighted hessian matrix, as calculated using HF/6-311+G(2d,2p) in Gaussian G09. The mathematics simple used a submatrix of the atoms of interest...
26 October 2015 891 7 View
On writing down the Hamiltonian for the particle-in-a-ring problem, and solving the Schrodinger to get the quantized energy in terms of the radius (R) of the ring, for the two examples of Benzene...
24 October 2015 5,884 3 View