Hi,

I would recommend GROMACS for a best MD simulation experience.

Regards,

SQ

GROMACS and NAMD are both widely used. Desmond seems not as prevalent as the other two, but all three have good reputations. GROMACS has the fewest restrictions on its use. NAMD has executables available for Linux, Mac, and Windows, whereas GROMACS must be compiled from source. Desmond is available as a linux binary or as source code; it also has a commercial version available from Schrodinger.

The MD code that you use depends at least somewhat on your research question that you are trying to answer by running MD simulations. You should also look into the requirements of each code for enabling acceleration through the use of the GPUs in your computer. GROMACS, NAMD, and Desmond make use of CUDA cores.

In my own case, at present I mainly use YASARA-Structure for MD simulations in explicit solvent. With this software, it is very easy to set up the simulations and to analyze and visualize the results. There are binary executables available for Linux, Mac, and Windows. The graphics are excellent and the interface is highly intuitive. GPU acceleration is accomplished with OpenCL rather than CUDA. YASARA-Structure is commercial software, but academic licenses are very reasonably priced and the licensing policies are extremely liberal.

Many thanks Sahar Qazi and Rudy J Richardson , my goal is to model the lowest energy secondary structure of these peptides without solvent.

You will find an extensive literature on experimental and computational studies of peptides of varying length and composition.

A 16-mer peptide consisting of all alanine residues will form predominantly alpha-helical structures in vacuo.

You might wish to compare your results with those obtained using the Pep-Fold server:

http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD/

An interesting publication may be found here:

Article Molecular dynamics simulations of the folding of poly(alanin...

Thank you again Rudy J Richardson ,yes I am aware of the literature regarding polyalanine helices. However, I am interested in multiply charged alanine sequences with varying positions of lysine, for which there is no model to my knowledge yet.

Thank you for the additional information that you are interested in peptides containing both alanine and lysine, with varying positions for the lysine residue(s).

I have seen a paper on the "KAK" peptide; you have probably seen this as well.

Depending on what you have in mind, I should think it would be of interest to do the simulations in explicit solvent as well as in vacuo.

In addition, you could still submit your peptides to the Pep-Fold server.

Rudy J Richardson What would be a starting structure for these polyalanine peptides after I type out the aminoacid sequence?

You could build the peptide using a molecular modeling program that includes energy minimization. After building the peptide, you could start with an energy minimization, which mainly serves to help ensure that the angles, orders, and lengths of all the bonds are correct. Then you could import this starting structure into your MD program. Alternatively, you could submit the peptide to the Pep-Fold web server to get predictions of secondary structure and start from there. However, for a 16-mer peptide, expecting it to fold correctly will likely have you waiting for a very long time.

I would recommend GROMACS for a best MD simulation for small molecule

Regards,