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Creating input file for coarse-grained model
02-23-2012, 09:57 AM
Post: #1
Creating input file for coarse-grained model
Hi Feng,

The default command " complex.linux -P paramDir -I complexPDB -D dimension -p outParam -s outstate " is for creating the input files for all-atom protein model, right? If I want to create input files for 4 bead or Quasi-all-atom model, can you provide me with some examples on how to create it? Thanks.

Andy
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02-28-2012, 12:35 AM
Post: #2
RE: Creating input file for coarse-grained model
Hi Andy,

We do not currently have an executable for creating input files for coarse-grained models, but piDMD has the ability to use any model of the user's creation. Please see section 3.4 of the User's Guide for step-by-step instructions for how to create these files for implementations of 1-bead, 2-bead, 4-bead, and quasi-all-atom protein models created in our lab, as well as our 3-bead models for RNA, DNA, and lipids.

Best regards,

Elizabeth

(02-23-2012 09:57 AM)andyng Wrote:  Hi Feng,

The default command " complex.linux -P paramDir -I complexPDB -D dimension -p outParam -s outstate " is for creating the input files for all-atom protein model, right? If I want to create input files for 4 bead or Quasi-all-atom model, can you provide me with some examples on how to create it? Thanks.

Andy
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