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...

05 June 2019 3,374 9 View

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

04 May 2019 7,871 3 View

How to create topology for a unique structure?

i have some structure that doesn't have any similar topology in charmm22 (protein) & charmm 27 (lipid) and i have tried several servers such as, cgenff & swiss param, but the .rtf file...

10 November 2018 8,340 3 View

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 422 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?

i interested in achieve delta(g) and I have read tutorial for fep but i didn't get useful information about creating input file.

09 October 2018 6,684 9 View

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

i tried on charmm-gui site but an error appears, what should i do? is there another way to calculate that?

01 February 2018 9,540 6 View

Hi all, does anybody have charmm program?

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

01 February 2018 3,560 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 8,786 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 5,299 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 5,306 4 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

Could you recommend any books about Number Theory?

Beginner level books. High level books. Analytical Number Theory. Algebraic Number Theory. Combinatorical Number Theory. Books about partitions. Books about primes.

03 March 2021 7,174 5 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View