Re: Question about Radius of hexagon;

From: Ramon Mendoza Uriarte (ramendoza_at_uchicago.edu)
Date: Thu Dec 24 2020 - 13:54:06 CST

Hi Seke,

It seems to me that you are using the CHARMM-GUI generated namd config files. For this to work you need to use this file:

step5_assembly.str

and is usually located above the namd directory. For example, the contents of this file look as follows:

SET BOXTYPE = RECT
SET XTLTYPE = TETRAGONAL
SET A = 76.1019214
SET B = 76.1019214
SET C = 92.454
SET ALPHA = 90.0
SET BETA = 90.0
SET GAMMA = 90.0
SET ZCEN = 0.0
SET NLIPTOP = 60
SET NLIPBOT = 52
SET NWATER = 9322
SET POSID = POT
SET NEGID = CLA
SET NPOS = 61
SET NNEG = 24

So, the FATAL ERROR: can't read "boxtype" is due to you not using this file. This section in your config file:

# read system values written by CHARMM (need to convert uppercases to lowercases)
exec tr "\[:upper:\]" "\[:lower:\]" < ../step5_assembly.str | sed -e "s/ =//g" > step5_charmm2namd.str
source step5_charmm2namd.str

takes the contents of step5_assembly.str and lowercases the things that are uppercase and outputs it into a new file called step5_charmm2namd.str ​and finally sources those specified values​.

POSSIBLE SOLUTION: So, all you need to do is add the step5_assembly.str ​file to the directory above the one you are working in (requires no modification of your current config file).

Alternatively, you could add the step5_assembly.str file ​to the directory you are working in, however this requires modification to the config file like so:

# read system values written by CHARMM (need to convert uppercases to lowercases)
exec tr "\[:upper:\]" "\[:lower:\]" < ../step5_assembly.str | sed -e "s/ =//g" > step5_charmm2namd.str
source step5_charmm2namd.str

to

# read system values written by CHARMM (need to convert uppercases to lowercases)
exec tr "\[:upper:\]" "\[:lower:\]" < step5_assembly.str | sed -e "s/ =//g" > step5_charmm2namd.str
source step5_charmm2namd.str

I think this should get your simulation running. I would advise against changing the config file as you want to do now. Try this first!

-Ramon
________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Seke Keretsu <sekekeretsu_at_gmail.com>
Sent: Wednesday, December 23, 2020 11:33 PM
To: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>
Subject: namd-l: Question about Radius of hexagon;

Dear Expert,

I have trouble finding the radius of Hexagon to set the conditions for PBC. If already discussed before, kindly pass me the reference.

I understand the values can be set as.

V1=( r; 0; 0)
V2= (r/2; sqrt (3)*r/2; 0)
V3= (0, 0, H)

But how do I find the value of r (min radius of hexagon)?

Thank you.

Sincerely, Seke

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