[gmx-users] PME update
asasa qsqs
sanaz_dr_m at yahoo.com
Mon Jan 19 01:44:59 CET 2015
Dear Justin,I studied KALP15 in DPPC, would you please help me? I want to know how often PME was updated in this tutorial? every 10th time step? How can i know?Many thanks,Mrs.Mahdavi
On Sunday, January 18, 2015 9:57 PM, "gromacs.org_gmx-users-request at maillist.sys.kth.se" <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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Today's Topics:
1. Decomposing the long range term of interaction energy
(Diogo Martins de =?UTF-8?Q?S=C3=A1?=)
2. Re: Decomposing the long range term of interaction energy
(David van der Spoel)
3. adding new residue (fatemeh ramezani)
----------------------------------------------------------------------
Message: 1
Date: Sun, 18 Jan 2015 06:07:41 -0700
From: "Diogo Martins de =?UTF-8?Q?S=C3=A1?=" <sadiogo at mol.bio.br>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Decomposing the long range term of interaction
energy
Message-ID:
<20150118060741.9fb2472ef9329f096e098461db973df3.618ccf3321.wbe at email14.secureserver.net>
Content-Type: text/plain; charset="utf-8"
I've been reading many tentatives of breaking down the long range term
of interaction, but have not found a feedback if any actually worked. Is
there a working method of achieving this?
Att.
Diogo
------------------------------
Message: 2
Date: Sun, 18 Jan 2015 15:48:37 +0100
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Decomposing the long range term of
interaction energy
Message-ID: <54BBC7C5.9060103 at xray.bmc.uu.se>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 2015-01-18 14:07, Diogo Martins de S? wrote:
> I've been reading many tentatives of breaking down the long range term
> of interaction, but have not found a feedback if any actually worked. Is
> there a working method of achieving this?
>
> Att.
>
> Diogo
>
We have done it and published the method in the supporting info of this
paper http://pubs.acs.org/doi/abs/10.1021/ct400404q
How useful it is depends on your system I guess.
Paper is interesting too :).
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
------------------------------
Message: 3
Date: Sun, 18 Jan 2015 18:26:27 +0000 (UTC)
From: fatemeh ramezani <fr_750 at yahoo.com>
To: "gmx-users-owner at gromacs.org" <gmx-users-owner at gromacs.org>,
"gmx-users-request at gromacs.org" <gmx-users-request at gromacs.org>,
"gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: [gmx-users] adding new residue
Message-ID:
<488796205.2916602.1421605587462.JavaMail.yahoo at jws10640.mail.bf1.yahoo.com>
Content-Type: text/plain; charset=UTF-8
Dear gmx-usersI want to simulate collagen molecule by gromacs. I produce hydroxyprolin parameter by swissparam site:
; ----
; Built itp for zinc_901791.mol2
;??? by user vzoete???? Mon Jan 12 11:37:34 CET 2015
; ----
;
[ atomtypes ]
; name at.num? mass?? charge? ptype??? sigma??????????? epsilon
CR????? 6?? 12.0110? 0.0? A???????? 0.387541??? 0.230120?
HCMM??? 1??? 1.0079? 0.0? A???????? 0.235197??? 0.092048
CO2M??? 6?? 12.0110? 0.0? A???????? 0.356359??? 0.292880?
O2CM??? 8?? 15.9994? 0.0? A???????? 0.302905??? 0.502080?
OR????? 8?? 15.9994? 0.0? A???????? 0.315378??? 0.636386?
HOR???? 1??? 1.0079? 0.0? A???????? 0.040001??? 0.192464?
NRP???? 7?? 14.0067? 0.0? A???????? 0.329632??? 0.836800
HNRP??? 1??? 1.0079? 0.0? A???????? 0.040001??? 0.192464?
[ pairtypes ]
;? i???? j??? func???? sigma1-4?????? epsilon1-4 ; THESE ARE 1-4 INTERACTIONS
CR?????? CR???? 1????? 0.338541??? 0.041840
CR?????? HCMM?? 1????? 0.286869??? 0.062059
CR?????? CO2M?? 1????? 0.347450??? 0.110698
CR?????? O2CM?? 1????? 0.320723??? 0.144938
CR?????? OR???? 1????? 0.326960??? 0.163176
CR?????? HOR??? 1????? 0.189271??? 0.089737
CR?????? NRP??? 1????? 0.334087??? 0.187114
CR?????? HNRP?? 1????? 0.189271??? 0.089737
[ moleculetype ]
; Name nrexcl
zinc_901791 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
?? 1 CR?? 1? LIG C1????? 1? 0.0000? 12.0110
?? 2 CR?? 1? LIG C2????? 2? 0.2800? 12.0110
?? 3 HCMM 1? LIG H1????? 3? 0.0000?? 1.0079
?? 4 CR?? 1? LIG C3????? 4? 0.5030? 12.0110
?? 5 CR?? 1? LIG C4????? 5? 0.3970? 12.0110
?? 6 HCMM 1? LIG H2????? 6? 0.0000?? 1.0079
?? 7 CO2M 1? LIG C5????? 7? 0.9060? 12.0110
?? 8 O2CM 1? LIG O1????? 8 -0.9000? 15.9994
?? 9 OR?? 1? LIG O2????? 9 -0.6800? 15.9994
? 10 HCMM 1? LIG H3???? 10? 0.0000?? 1.0079
? 11 HCMM 1? LIG H4???? 11? 0.0000?? 1.0079
? 12 HCMM 1? LIG H5???? 12? 0.0000?? 1.0079
? 13 HCMM 1? LIG H6???? 13? 0.0000?? 1.0079
? 14 HOR? 1? LIG H7???? 14? 0.4000?? 1.0079
? 15 NRP? 1? LIG N1???? 15 -0.9060? 14.0067
? 16 HNRP 1? LIG H8???? 16? 0.4500?? 1.0079
? 17 HNRP 1? LIG H9???? 17? 0.4500?? 1.0079
? 18 O2CM 1? LIG O3???? 18 -0.9000? 15.9994
[ bonds ]
; ai aj fu b0 kb, b0 kb
? 7?? 8 1 0.12610? 587519.8? 0.12610? 587519.8
? 7? 18 1 0.12610? 587519.8? 0.12610? 587519.8
? 1?? 5 1 0.15080? 256422.3? 0.15080? 256422.3
? 1?? 2 1 0.15080? 256422.3? 0.15080? 256422.3
? 1? 10 1 0.10930? 287014.9? 0.10930? 287014.9
? 1? 11 1 0.10930? 287014.9? 0.10930? 287014.9
? 2?? 3 1 0.10930? 287014.9? 0.10930? 287014.9
? 2?? 4 1 0.15080? 256422.3? 0.15080? 256422.3
? 2?? 9 1 0.14180? 303937.5? 0.14180? 303937.5
? 4? 12 1 0.10930? 287014.9? 0.10930? 287014.9
? 4? 13 1 0.10930? 287014.9? 0.10930? 287014.9
? 4? 15 1 0.14800? 231490.7? 0.14800? 231490.7
? 5?? 6 1 0.10930? 287014.9? 0.10930? 287014.9
? 5?? 7 1 0.15100? 230648.0? 0.15100? 230648.0
? 5? 15 1 0.14800? 231490.7? 0.14800? 231490.7
? 9? 14 1 0.09720? 469365.3? 0.09720? 469365.3
?15? 16 1 0.10280? 371144.2? 0.10280? 371144.2
?15? 17 1 0.10280? 371144.2? 0.10280? 371144.2
[ pairs ]
; ai aj fu
? 1? 12 1?
? 1? 13 1?
? 1? 14 1?
? 1?? 8 1?
? 1? 18 1?
? 1? 16 1?
? 1? 17 1?
? 2?? 6 1?
? 2?? 7 1?
? 2? 16 1?
? 2? 17 1?
? 3?? 5 1?
? 3? 10 1?
? 3? 11 1?
? 3? 12 1?
? 3? 13 1?
? 3? 15 1?
? 3? 14 1?
? 4? 10 1?
? 4? 11 1?
? 4? 14 1?
? 4?? 6 1?
? 4?? 7 1?
? 5?? 9 1?
? 5? 12 1?
? 5? 13 1?
? 6? 10 1?
? 6? 11 1?
? 6?? 8 1?
? 6? 18 1?
? 6? 16 1?
? 6? 17 1?
? 7? 10 1?
? 7? 11 1?
? 7? 16 1?
? 7? 17 1?
? 8? 15 1?
? 9? 10 1?
? 9? 11 1?
? 9? 12 1?
? 9? 13 1?
? 9? 15 1?
?10? 15 1?
?11? 15 1?
?12? 16 1?
?12? 17 1?
?13? 16 1?
?13? 17 1?
?15? 18 1?
[ angles ]
; ai aj ak fu th0 kth ub0 kub th0
? 2?? 1?? 5 1? 109.6080? 512.48
? 2?? 1? 10 1? 110.5490? 383.00
? 2?? 1? 11 1? 110.5490? 383.00
? 5?? 1? 10 1? 110.5490? 383.00
? 5?? 1? 11 1? 110.5490? 383.00
?10?? 1? 11 1? 108.8360? 310.74
? 1?? 2?? 3 1? 110.5490? 383.00
? 1?? 2?? 4 1? 109.6080? 512.48
? 1?? 2?? 9 1? 108.1330? 597.39
? 3?? 2?? 4 1? 110.5490? 383.00
? 3?? 2?? 9 1? 108.5770? 470.32
? 4?? 2?? 9 1? 108.1330? 597.39
? 2?? 4? 12 1? 110.5490? 383.00
? 2?? 4? 13 1? 110.5490? 383.00
? 2?? 4? 15 1? 106.4930? 710.01
?12?? 4? 13 1? 108.8360? 310.74
?12?? 4? 15 1? 106.2240? 525.13
?13?? 4? 15 1? 106.2240? 525.13
? 1?? 5?? 6 1? 110.5490? 383.00
? 1?? 5?? 7 1?? 98.4220? 198.73
? 1?? 5? 15 1? 106.4930? 710.01
? 6?? 5?? 7 1? 108.9040? 316.16
? 6?? 5? 15 1? 106.2240? 525.13
? 7?? 5? 15 1? 112.2380? 631.11
? 5?? 7?? 8 1? 114.6890? 728.07
? 5?? 7? 18 1? 114.6890? 728.07
? 8?? 7? 18 1? 130.6000? 711.20
? 2?? 9? 14 1? 106.5030? 477.55
? 4? 15?? 5 1? 112.2510? 519.10
? 4? 15? 16 1? 111.2060? 346.87
? 4? 15? 17 1? 111.2060? 346.87
? 5? 15? 16 1? 111.2060? 346.87
? 5? 15? 17 1? 111.2060? 346.87
?16? 15? 17 1? 107.7870? 348.08
[ dihedrals ]
; ai aj ak al fu phi0 kphi mult phi0
? 1?? 2?? 4? 12 9?? 0.00?? 1.3389 1
? 1?? 2?? 4? 12 9 180.00? -1.3180 2
? 1?? 2?? 4? 12 9?? 0.00?? 0.5523 3
? 1?? 2?? 4? 13 9?? 0.00?? 1.3389 1
? 1?? 2?? 4? 13 9 180.00? -1.3180 2
? 1?? 2?? 4? 13 9?? 0.00?? 0.5523 3
? 1?? 2?? 4? 15 9?? 0.00? -1.3556 1
? 1?? 2?? 4? 15 9 180.00?? 1.1506 2
? 1?? 2?? 4? 15 9?? 0.00?? 1.2343 3
? 1?? 2?? 9? 14 9 180.00?? 0.5648 2
? 1?? 2?? 9? 14 9?? 0.00?? 0.4937 3
? 1?? 5?? 7?? 8 9 180.00?? 2.6401 2
? 1?? 5?? 7? 18 9 180.00?? 2.6401 2
? 1?? 5? 15?? 4 9?? 0.00?? 0.5230 3
? 1?? 5? 15? 16 9?? 0.00?? 0.3891 3
? 1?? 5? 15? 17 9?? 0.00?? 0.3891 3
? 2?? 1?? 5?? 6 9?? 0.00?? 1.3389 1
? 2?? 1?? 5?? 6 9 180.00? -1.3180 2
? 2?? 1?? 5?? 6 9?? 0.00?? 0.5523 3
? 2?? 1?? 5?? 7 9?? 0.00?? 0.6276 3
? 2?? 1?? 5? 15 9?? 0.00? -1.3556 1
? 2?? 1?? 5? 15 9 180.00?? 1.1506 2
? 2?? 1?? 5? 15 9?? 0.00?? 1.2343 3
? 2?? 4? 15?? 5 9?? 0.00?? 0.5230 3
? 2?? 4? 15? 16 9?? 0.00?? 0.3891 3
? 2?? 4? 15? 17 9?? 0.00?? 0.3891 3
? 3?? 2?? 1?? 5 9?? 0.00?? 1.3389 1
? 3?? 2?? 1?? 5 9 180.00? -1.3180 2
? 3?? 2?? 1?? 5 9?? 0.00?? 0.5523 3
? 3?? 2?? 1? 10 9?? 0.00?? 0.5941 1
? 3?? 2?? 1? 10 9 180.00? -2.8995 2
? 3?? 2?? 1? 10 9?? 0.00?? 0.6569 3
? 3?? 2?? 1? 11 9?? 0.00?? 0.5941 1
? 3?? 2?? 1? 11 9 180.00? -2.8995 2
? 3?? 2?? 1? 11 9?? 0.00?? 0.6569 3
? 3?? 2?? 4? 12 9?? 0.00?? 0.5941 1
? 3?? 2?? 4? 12 9 180.00? -2.8995 2
? 3?? 2?? 4? 12 9?? 0.00?? 0.6569 3
? 3?? 2?? 4? 13 9?? 0.00?? 0.5941 1
? 3?? 2?? 4? 13 9 180.00? -2.8995 2
? 3?? 2?? 4? 13 9?? 0.00?? 0.6569 3
? 3?? 2?? 4? 15 9?? 0.00?? 1.4477 1
? 3?? 2?? 4? 15 9 180.00? -1.1088 2
? 3?? 2?? 4? 15 9?? 0.00?? 0.5816 3
? 3?? 2?? 9? 14 9?? 0.00?? 1.2468 1
? 3?? 2?? 9? 14 9 180.00? -0.5774 2
? 3?? 2?? 9? 14 9?? 0.00?? 0.7238 3
? 4?? 2?? 1?? 5 9?? 0.00?? 0.2134 1
? 4?? 2?? 1?? 5 9 180.00?? 1.4267 2
? 4?? 2?? 1?? 5 9?? 0.00?? 0.6945 3
? 4?? 2?? 1? 10 9?? 0.00?? 1.3389 1
? 4?? 2?? 1? 10 9 180.00? -1.3180 2
? 4?? 2?? 1? 10 9?? 0.00?? 0.5523 3
? 4?? 2?? 1? 11 9?? 0.00?? 1.3389 1
? 4?? 2?? 1? 11 9 180.00? -1.3180 2
? 4?? 2?? 1? 11 9?? 0.00?? 0.5523 3
? 4?? 2?? 9? 14 9 180.00?? 0.5648 2
? 4?? 2?? 9? 14 9?? 0.00?? 0.4937 3
? 4? 15?? 5?? 6 9?? 0.00?? 0.5146 3
? 4? 15?? 5?? 7 9?? 0.00?? 0.5230 3
? 5?? 1?? 2?? 9 9?? 0.00? -1.4393 1
? 5?? 1?? 2?? 9 9 180.00?? 3.6777 2
? 5?? 1?? 2?? 9 9?? 0.00?? 0.9958 3
? 5? 15?? 4? 12 9?? 0.00?? 0.5146 3
? 5? 15?? 4? 13 9?? 0.00?? 0.5146 3
? 6?? 5?? 1? 10 9?? 0.00?? 0.5941 1
? 6?? 5?? 1? 10 9 180.00? -2.8995 2
? 6?? 5?? 1? 10 9?? 0.00?? 0.6569 3
? 6?? 5?? 1? 11 9?? 0.00?? 0.5941 1
? 6?? 5?? 1? 11 9 180.00? -2.8995 2
? 6?? 5?? 1? 11 9?? 0.00?? 0.6569 3
? 6?? 5?? 7?? 8 9?? 0.00? -0.2218 3
? 6?? 5?? 7? 18 9?? 0.00? -0.2218 3
? 6?? 5? 15? 16 9?? 0.00?? 0.5439 3
? 6?? 5? 15? 17 9?? 0.00?? 0.5439 3
? 7?? 5?? 1? 10 9?? 0.00? -0.2929 3
? 7?? 5?? 1? 11 9?? 0.00? -0.2929 3
? 7?? 5? 15? 16 9?? 0.00?? 0.5230 3
? 7?? 5? 15? 17 9?? 0.00?? 0.5230 3
? 8?? 7?? 5? 15 9 180.00?? 1.2552 2
? 9?? 2?? 1? 10 9?? 0.00? -1.3682 1
? 9?? 2?? 1? 10 9 180.00?? 2.2426 2
? 9?? 2?? 1? 10 9?? 0.00?? 0.5858 3
? 9?? 2?? 1? 11 9?? 0.00? -1.3682 1
? 9?? 2?? 1? 11 9 180.00?? 2.2426 2
? 9?? 2?? 1? 11 9?? 0.00?? 0.5858 3
? 9?? 2?? 4? 12 9?? 0.00? -1.3682 1
? 9?? 2?? 4? 12 9 180.00?? 2.2426 2
? 9?? 2?? 4? 12 9?? 0.00?? 0.5858 3??
? 9?? 2?? 4? 13 9?? 0.00? -1.3682 1
? 9?? 2?? 4? 13 9 180.00?? 2.2426 2
? 9?? 2?? 4? 13 9?? 0.00?? 0.5858 3
? 9?? 2?? 4? 15 9?? 0.00?? 0.6276 3
?10?? 1?? 5? 15 9?? 0.00?? 1.4477 1
?10?? 1?? 5? 15 9 180.00? -1.1088 2
?10?? 1?? 5? 15 9?? 0.00?? 0.5816 3
?11?? 1?? 5? 15 9?? 0.00?? 1.4477 1
?11?? 1?? 5? 15 9 180.00? -1.1088 2
?11?? 1?? 5? 15 9?? 0.00?? 0.5816 3
?12?? 4? 15? 16 9?? 0.00?? 0.5439 3
?12?? 4? 15? 17 9?? 0.00?? 0.5439 3
?13?? 4? 15? 16 9?? 0.00?? 0.5439 3
?13?? 4? 15? 17 9?? 0.00?? 0.5439 3
?15?? 5?? 7? 18 9 180.00?? 1.2552 2
[ dihedrals ]
; ai aj ak al fu xi0 kxi xi0 kxi
? 1?? 2?? 5? 10 2?? 0.00?? 0.0000
? 1?? 2?? 5? 11 2?? 0.00?? 0.0000
? 2?? 4?? 1?? 9 2?? 0.00?? 0.0000
? 2?? 4?? 1?? 3 2?? 0.00?? 0.0000
? 5?? 7?? 1? 15 2?? 0.00?? 0.0000
? 5?? 7?? 1?? 6 2?? 0.00?? 0.0000
? 7?? 8?? 5? 18 2?? 0.00 107.1941
? 4? 15?? 2? 12 2?? 0.00?? 0.0000
? 4? 12?? 2? 13 2?? 0.00?? 0.0000
?15?? 4?? 5? 16 2?? 0.00?? 0.0000
?15?? 4?? 5? 17 2?? 0.00?? 0.0000
#ifdef POSRES_LIGAND
[ position_restraints ]
; atom? type????? fx????? fy????? fz
?? 1 1 1000 1000 1000
?? 2 1 1000 1000 1000
?? 4 1 1000 1000 1000
?? 5 1 1000 1000 1000
?? 7 1 1000 1000 1000
?? 8 1 1000 1000 1000
?? 9 1 1000 1000 1000
? 15 1 1000 1000 1000
? 18 1 1000 1000 1000
#endif
I added atomtypes section in .atp file. I added hydroxyprolin hydrogen data in hdb file.
I dded [bonds], [angles], [dihedrals] and 2th [dihedrals] in ffbonded.itp file respectively in [ bondtypes ], [ anglestypes ], [dihedraltypes ] and 2th [dihedraltypes ].in the first grompp, this error appeared:number of coordinates in coordinate file (x.pdb, 72323)
???????????? does not match topology (x.top, 95870)
that the difference is equal to sol atom number that is 23547I dont know how can I solve this problem. I appreciate any help.
?Fatemeh Ramezani
------------------------------
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