Hi Feng:
I'm trying to follow your instruction and run a short SMD without harmonic restraint. Right now my md.in and cv.in looks like:
md.in:
Restrain all backbone CA atoms
10.0
ATOM 5 5
...... ...... ......
...... ...... ......
ATOM 4367 4367
END
END
/
&smd
output_file = 'xx_smd.txt'
output_freq = 10000
cv_file= 'cv.in'
/
Everything else in md.in remains unchanged.
cv.in:
cv_file
&colvar
cv_type = 'MULTI_RMSD'
cv_ni = 14, cv_nr = 36
cv_i = (4618, 4636, 4632, 4628, 4621, 4620, 0, 4646, 4664, 4660, 4656, 4649, 4648, 0)
cv_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)
npath = 2, path = 1, 0, path_mode = 'LINES',
nharm = 1, harm = 0.0
/
My goal is to steer the MULTI_RMSD value to zero(whatever the starting value is). The value 1 in "path" is just arbitrary, because "path" needs to contain at least two real numbers. Now I get the following error:
5. REFERENCE ATOM COORDINATES
default_name
----- READING GROUP 1; TITLE:
GROUP 1 HAS HARMONIC CONSTRAINTS 0.00000
rfree: End of file on unit 5
Since the message says the group has Harm of 0.0, I know its the SMD cv_r group rather than the previous cartesian restraint group.
Could you offer more instructions?
Many thanks
Yao
________________________________
·¢¼þÈË: Feng Pan <fpan3.ncsu.edu>
·¢ËÍʱ¼ä: 2017Äê7ÔÂ24ÈÕ 22:27:45
ÊÕ¼þÈË: AMBER Mailing List
Ö÷Ìâ: Re: [AMBER] ´ð¸´: ncsu_smd codes with pmemd in Amber 16
Hi, Yao
Yes, in the new format the "path" cannot contain a 'X' component according
to coding reasons. If you want to put the initial value into it, a
trick is that you can run a very short SMD with harm_strength equal zero,
check the monitor file and you can get the initial value.
For the GROUP, should be this part
Restrain all backbone CA atoms
10.0
ATOM 5 5
...... ...... ......
...... ...... ......
ATOM 4367 4367
END
END
As I know, you should put the END END just behind your group definitions.
Best
Feng
On Mon, Jul 24, 2017 at 5:55 PM, Yao Xiao <yao.xiao26.uga.edu> wrote:
> 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
>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Tue Jul 25 2017 - 13:00:02 PDT
