Can anybody help me with the working of NAMD or Desmond for molecular dynamics study of proteins???
Many thanx in advance.
Dear nutan
I will prefer you first you just read the theory about the MD simulation, than you can understand what is this ? after that you used to start to do M D simulation. i can just tell u the how you can finish your task. for handling the s/w i will give direction only bez i am not able to make you hands on experience. so follow the instruction of manual of NAMD it very easy to handle if you if any difficulties just send me a mail.
All the Best
Saurabh Gupta
M.Tech (Bio informatics),B. Tech (Biotechnology)
Research scholar
Bioinformatics, Applied Science Division & IRCB
Indian Institute of Information Technology
Allahabad-211012, India
Dear nutan
which type of the simulation u want to do, i mean to say vacuum or with water. please can be specific ?
there are other many s/w by which u can easily do the simulation .
Saurabh gupta
Thanx for reply dear,
Actually I dnt have any good idea regarding MD studies...means what condition should i use and why coz i just started studying it? :( I have to do MD of my protein so was trying NAMD and also downloaded Desmond..but have no idea about. Could you please help me in this regard.
Many thanx
Dear nutan
I will prefer you first you just read the theory about the MD simulation, than you can understand what is this ? after that you used to start to do M D simulation. i can just tell u the how you can finish your task. for handling the s/w i will give direction only bez i am not able to make you hands on experience. so follow the instruction of manual of NAMD it very easy to handle if you if any difficulties just send me a mail.
All the Best
Saurabh Gupta
M.Tech (Bio informatics),B. Tech (Biotechnology)
Research scholar
Bioinformatics, Applied Science Division & IRCB
Indian Institute of Information Technology
Allahabad-211012, India
Agree. Read a good book on MD (like "Understanding Molecular Simulation" by Frenkel and Smit) BEFORE starting. Then choose the software you prefer -NAMD or Gromacs are both good choices.
I've not used Gromacs myself, but it's supposed to be good if you're limited to a desktop. I used to use CHARMM, but I've moved onto NAMD as it parallelizes well.
There are good tutorials on the NAMD website. They also have a searchable tutorial mailing list as well as a wiki (http://www.ks.uiuc.edu/Research/namd/wiki/). But you might also want to get on mailing lists or join forums, such as the CHARMM forum, where theory as well as methods get discussed irrespective of the program you choose.
If you want a more accessible text book I would suggest the following two:
A. Leach, Molecular Modelling Principles and Applications - http://www.amazon.com/Molecular-Modelling-Principles-Applications-2nd/dp/0582382106
T. Schlick, Molecular Modeling and Simulation - http://www.amazon.com/gp/product/038795404X/ref=pd_lpo_k2_dp_sr_1?pf_rd_p=486539851&pf_rd_s=lpo-top-stripe-1&pf_rd_t=201&pf_rd_i=0582382106&pf_rd_m=ATVPDKIKX0DER&pf_rd_r=16WB83N5DTGD4WPTX8HX
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