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
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
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01 February 2019 7,874 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
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
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
Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...
06 August 2024 1,495 2 View
kindly reply me. Thanking you in advance.
05 August 2024 7,727 4 View
I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...
04 August 2024 1,200 2 View
Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...
03 August 2024 3,371 3 View
I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?
02 August 2024 3,143 4 View
Molecular docking software/ websites?
02 August 2024 8,704 7 View
Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...
31 July 2024 781 1 View
Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...
29 July 2024 1,092 2 View
Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar
29 July 2024 3,084 8 View