Hi, Feng:
Thank you very much for your help.
Yes, I notice the new input format in amber manual 17, but I still have the some questions:
In the old ncsu_smd format, "path" can contain X, which means the intital value of the reaction coordinate. How can I express this concept of initial value in the new input format? According to the manual, "path" must contain real numbers. Obviously I don't know the initial value beforehand.
Also, could you please elaborate on the "GROUP definition? Does that mean the content between "&something" and "/"? In other words, does the former initializes, while the latter ends a group definition? I'm a beginner user of Amber so I need some more instructions.
Thanks.
Best,
Yao
________________________________
·¢¼þÈË: Feng Pan <fpan3.ncsu.edu>
·¢ËÍʱ¼ä: 2017Äê7ÔÂ24ÈÕ 17:11:33
ÊÕ¼þÈË: AMBER Mailing List
Ö÷Ìâ: Re: [AMBER] ncsu_smd codes with pmemd in Amber 16
Hi, Yao
The SMD in pmemd uses a new &smd input format, so you need to change the
input styles. Check
the new Amber 2017 manual for details.
Also, I think you cannot put the SMD block inside the group block. You
should finish the GROUP definition
first and then write &smd block.
Best
Feng
On Mon, Jul 24, 2017 at 4:58 PM, Yao Xiao <yao.xiao26.uga.edu> wrote:
> Dear Amber Developers:
>
>
> I'm trying to use the ncsu_smd codes for steered MD. Basically I want to
> steer two Glcnac rings to their positions in a known crystal structure.
> Below is my MD input file:
>
>
> MD production run at NPT
> # control section
> &cntrl
> irest = 1,
> ntx = 5, ntb = 2, ntp = 1,ntwprt=4675
> cut = 8.0, ntt = 3, gamma_ln = 2,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0, tautp = 2.0,
> nstlim = 100000000, dt = 0.002,
> ntpr = 30000, ntwx = 10000, ntwv = 0, ntwe = 0,
> nmropt = 0, ntr=1, ioutfm =1,iwrap=1,ig = -1,
> /
> Restrain all backbone CA atoms
> 10.0
> ATOM 5 5
> ...... ...... ......
> ...... ...... ......
> ATOM 4367 4367
>
> /
> ncsu_smd
> output_file = 'xx_smd.txt'
> output_freq = 10000
> variable
> type= MULTI_RMSD
> i=(4618, 4636, 4632, 4628, 4621, 4620, 0, 4646, 4664, 4660, 4656,
> 4649, 4648, 0)
> r=(47.228, 38.993, 29.383,
> 48.172, 39.346, 30.539,
> 47.472, 40.312, 31,486,
> 47.010, 41.547, 30.733,
> 46.155, 41.145, 29.525,
> 46.917, 40.161, 28.700,
>
> 46.955, 30.894, 40.394,
> 47.928, 31.919, 41.011,
> 49.322, 31.437, 40.654,
> 49.559, 30.004, 41.103,
> 48.484, 29.062, 40.595,
> 47.239, 29.616, 40.816)
>
> path = (X,0) path_mode = LINES
>
> harm = (10.0)
>
> end variable
> end ncsu_smd
>
> END
> END
>
>
> The atom id of the Glcnac rings are defined in "i=" session, and the
> target coordinates are defined in "r=" session. By submitting a pmemd job
> with this input file I got the following error:
>
>
> 5. REFERENCE ATOM COORDINATES
>
> default_name
> ----- READING GROUP 1; TITLE:
> ncsu_smd
>
> rfree: Error decoding variable 1 3 from:
> output_file
>
> I know update 9 has to be applied for compatibility between ncsu_smd codes
> and pmemd, and I believe I've done that. Then, my MD input file must be
> wrong. My rationale for this MD input file come from Amber manual 16, page
> 434, figure 22.7.
>
> Could somebody help me figure out the issues? Thanks in advance.
>
> Best,
>
> Yao Xiao
> Research Assistant
> Complex Carbohydrate Research Center
> The University of Georgia
> Athens, GA USA
> yx55537.uga.edu
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 24 2017 - 15:00:02 PDT
