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 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 9,572 2 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

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

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 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