12 December 2017 2 10K Report

after creation initial parameter file, i stuck in second step that require optimization log file,

please help me, guys.

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What is the difference between normal cell membrane & cancerous cell membrane?

for example, I have used POPE cell membrane in my research work (molecular dynamics), but according to the paper that I attached below, this membrane is a kind of normal membrane. if there is...

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Hi NAMD users, I have an error that I described below... please tell me what should I do?

recently, I encountered an error at the beginning of the simulation, which related to Atom 3662, please let me know the solution of this error: FATAL ERROR: Atom 3662 has bad hydrogen group size. ...

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Hi all, please see this error message about namd config file and tell me what should i do to solve that?

# error message: TCL: can't read "temp": no such variable FATAL ERROR: can't read "temp": no such variable while executing "runFEPmin 0.0 0.0 0.0 $numSteps $numMinSteps $temp" (file...

09 October 2018 536 4 View

Hi all, I want to perform calculation of free energy <fep> for a drug in the water box. Is there somebody who can provide me with a input file?

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09 October 2018 6,793 9 View

Hi all, does anybody know about calculation of solvation free energy?

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01 February 2018 9,655 6 View

Hi all, does anybody have charmm program?

if someone have this software, I appreciate the one who send it.

01 February 2018 3,667 7 View

Hi everybody, i tried to obtain parameter file with cgenff but an error appears. what should i do?

the details of this error is shown below: (readmol2 warning: wildcard atom types not allowed; skipped molecule MOL2), also i tried another method such as swiss param website but i did not receive...

11 December 2017 8,925 4 View

Hi everybody, i tried to obtain parameter file with cgenff but an error appears. what should i do?

the details of this error is shown below: (readmol2 warning: wildcard atom types not allowed; skipped molecule MOL2), also i tried another method such as swiss param website but i did not receive...

11 December 2017 5,436 4 View

Hi everybody, i want to know how to create parameter file with fftk on vmd, can anybody help me?

after creation initial parameter file, i stuck in second step that require optimization log file, please help me, guys.

11 December 2017 5,417 4 View

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