[gmx-users] gromacs.org_gmx-users Digest, Vol 117, Issue 47
Hao Ren
renh.cn at gmail.com
Fri Jan 17 09:22:20 CET 2014
Hi Abhijit,
Thank you for your reply.
There is no negative frequencies in the output.
I am just running a test case, a Gly3 (GGG) in a vacuum box, to test
whether Gromacs can predict reasonable frequencies/normal modes for high
frequency vibrations.
The configuration, topology and md input files are attached.
I do not know whether I ran a correct simulation with appropriate
parameters or I just made some mistakes.
Could you please help me to check that?
Many thanks,
Hao
On Fri, Jan 17, 2014 at 7:56 AM, Hao Ren <renh.cn at gmail.com> wrote:
>> >Hi all,
>> >
>> >I am trying to do vibrational analysis for some high frequency modes in
>> >peptides (using force field method), such as the N-H stretching, C=O
>> >stretching, N-H bending, etc.
>> >
>> >However, I got some unreasonable large frequencies, 6,000-250,000
>> >wavenumbers, which are obviously not correct.
>> >
>> >Does anyone has experience on this issue? I just wanna know whether force
>> >filed can predict such kind of vibrations with frequencies usually in the
>> >range 1,000~3,000 wavenumbers.
>> >
>> >I appreciate any help and suggestions,
>> >Best Regards,
>> >Hao
>> >--
>> >Gromacs Users mailing list
>> >
>> >* Please search the archive athttp://www.gromacs.org/
>> >Support/Mailing_Lists/GMX-Users_List before posting!
>> >
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>> >
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>> >
>
> -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur
> ------------------------------ Message: 4 Date: Fri, 17 Jan 2014
> 10:42:59 +0530 From: abhijit Kayal <abhijitchemiitd at gmail.com> To:
> gmx-users at gromacs.org Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] normal mode analysis for high frequency
> vibrations Message-ID:
> <CANu9SWieiJA3Z4yv1Er0V3h=KSmWOhvJRdQTBzzFKRO=Ru2bOA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1 can you give me more
> details? Is there any negative frequency you have found?
-------------- next part --------------
TITLE
Generated by trjconv : t= 2001.00000
END
TIMESTEP
2001 2001.000000
END
POSITIONRED
1.252687648 1.507803820 1.568635478
1.259203580 1.408772387 1.536043672
1.235957032 1.503421507 1.667334163
1.175861423 1.548375383 1.517855464
1.376850079 1.578527067 1.534616510
1.376706665 1.677089621 1.581185829
1.463647807 1.524654395 1.572845634
1.383112326 1.595732319 1.383428479
1.312949932 1.681225006 1.330436651
1.459586377 1.509584435 1.316355412
1.494607052 1.432138589 1.373014884
1.456853919 1.486321939 1.171434618
1.394951695 1.559480672 1.119135002
1.557638491 1.493906285 1.130671834
1.402228672 1.345111035 1.145828715
1.318763806 1.325154359 1.058198196
1.438129843 1.252397537 1.235146770
1.507585299 1.278887782 1.304013319
1.341843006 1.169322565 1.305050354
1.242130769 1.171547356 1.260626812
1.376023546 1.066013366 1.310324871
1.341992931 1.232681447 1.444459196
1.233267034 1.262980383 1.497399087
1.447612126 1.286998716 1.485155011
END
BOX
2.729200000 2.729200000 2.729200000
END
-------------- next part --------------
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
define = -DFLEXIBLE
integrator = nm ; Algorithm (steep = steepest descent minimization)
constraints = none
emtol = 100.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
-------------- next part --------------
;
; File 'topol.top' was generated
; By user: ren (1000)
; On host: weissbier
; At date: Fri Jan 17 08:55:11 2014
;
; This is a standalone topology file
;
; It was generated using program:
; pdb2gmx_d - VERSION 4.6.3
;
; Command line was:
; pdb2gmx_d -f em.gro
;
; Force field was read from the standard Gromacs share directory.
;
; Include forcefield parameters
#include "oplsaa.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 GLY rtp GLY q +1.0
1 opls_287 1 GLY N 1 -0.3 14.0067 ; qtot -0.3
2 opls_290 1 GLY H1 1 0.33 1.008 ; qtot 0.03
3 opls_290 1 GLY H2 1 0.33 1.008 ; qtot 0.36
4 opls_290 1 GLY H3 1 0.33 1.008 ; qtot 0.69
5 opls_292B 1 GLY CA 1 0.19 12.011 ; qtot 0.88
6 opls_140 1 GLY HA1 1 0.06 1.008 ; qtot 0.94
7 opls_140 1 GLY HA2 1 0.06 1.008 ; qtot 1
8 opls_235 1 GLY C 2 0.5 12.011 ; qtot 1.5
9 opls_236 1 GLY O 2 -0.5 15.9994 ; qtot 1
; residue 2 GLY rtp GLY q 0.0
10 opls_238 2 GLY N 3 -0.5 14.0067 ; qtot 0.5
11 opls_241 2 GLY H 3 0.3 1.008 ; qtot 0.8
12 opls_223B 2 GLY CA 3 0.08 12.011 ; qtot 0.88
13 opls_140 2 GLY HA1 3 0.06 1.008 ; qtot 0.94
14 opls_140 2 GLY HA2 3 0.06 1.008 ; qtot 1
15 opls_235 2 GLY C 4 0.5 12.011 ; qtot 1.5
16 opls_236 2 GLY O 4 -0.5 15.9994 ; qtot 1
; residue 3 GLY rtp GLY q -1.0
17 opls_238 3 GLY N 5 -0.5 14.0067 ; qtot 0.5
18 opls_241 3 GLY H 5 0.3 1.008 ; qtot 0.8
19 opls_284 3 GLY CA 5 -0.02 12.011 ; qtot 0.78
20 opls_140 3 GLY HA1 5 0.06 1.008 ; qtot 0.84
21 opls_140 3 GLY HA2 5 0.06 1.008 ; qtot 0.9
22 opls_271 3 GLY C 6 0.7 12.011 ; qtot 1.6
23 opls_272 3 GLY O1 6 -0.8 15.9994 ; qtot 0.8
24 opls_272 3 GLY O2 6 -0.8 15.9994 ; qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
1 5 1
5 6 1
5 7 1
5 8 1
8 9 1
8 10 1
10 11 1
10 12 1
12 13 1
12 14 1
12 15 1
15 16 1
15 17 1
17 18 1
17 19 1
19 20 1
19 21 1
19 22 1
22 23 1
22 24 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 9 1
1 10 1
2 6 1
2 7 1
2 8 1
3 6 1
3 7 1
3 8 1
4 6 1
4 7 1
4 8 1
5 11 1
5 12 1
6 9 1
6 10 1
7 9 1
7 10 1
8 13 1
8 14 1
8 15 1
9 11 1
9 12 1
10 16 1
10 17 1
11 13 1
11 14 1
11 15 1
12 18 1
12 19 1
13 16 1
13 17 1
14 16 1
14 17 1
15 20 1
15 21 1
15 22 1
16 18 1
16 19 1
17 23 1
17 24 1
18 20 1
18 21 1
18 22 1
20 23 1
20 24 1
21 23 1
21 24 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1
2 1 4 1
2 1 5 1
3 1 4 1
3 1 5 1
4 1 5 1
1 5 6 1
1 5 7 1
1 5 8 1
6 5 7 1
6 5 8 1
7 5 8 1
5 8 9 1
5 8 10 1
9 8 10 1
8 10 11 1
8 10 12 1
11 10 12 1
10 12 13 1
10 12 14 1
10 12 15 1
13 12 14 1
13 12 15 1
14 12 15 1
12 15 16 1
12 15 17 1
16 15 17 1
15 17 18 1
15 17 19 1
18 17 19 1
17 19 20 1
17 19 21 1
17 19 22 1
20 19 21 1
20 19 22 1
21 19 22 1
19 22 23 1
19 22 24 1
23 22 24 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 5 6 3
2 1 5 7 3
2 1 5 8 3
3 1 5 6 3
3 1 5 7 3
3 1 5 8 3
4 1 5 6 3
4 1 5 7 3
4 1 5 8 3
1 5 8 9 3
1 5 8 10 3
6 5 8 9 3
6 5 8 10 3
7 5 8 9 3
7 5 8 10 3
5 8 10 11 3
5 8 10 12 3
9 8 10 11 3
9 8 10 12 3
8 10 12 13 3
8 10 12 14 3
8 10 12 15 3
11 10 12 13 3
11 10 12 14 3
11 10 12 15 3
10 12 15 16 3
10 12 15 17 3
13 12 15 16 3
13 12 15 17 3
14 12 15 16 3
14 12 15 17 3
12 15 17 18 3
12 15 17 19 3
16 15 17 18 3
16 15 17 19 3
15 17 19 20 3
15 17 19 21 3
15 17 19 22 3
18 17 19 20 3
18 17 19 21 3
18 17 19 22 3
17 19 22 23 3
17 19 22 24 3
20 19 22 23 3
20 19 22 24 3
21 19 22 23 3
21 19 22 24 3
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
5 10 8 9 1 improper_O_C_X_Y
8 12 10 11 1 improper_Z_N_X_Y
12 17 15 16 1 improper_O_C_X_Y
15 19 17 18 1 improper_Z_N_X_Y
19 23 22 24 1 improper_O_C_X_Y
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
[ system ]
; Name
Generated by trjconv : Protein in water t= 2038.00000
[ molecules ]
; Compound #mols
Protein 1
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