[gmx-users] PME update
Carsten Kutzner
ckutzne at gwdg.de
Mon Jan 19 07:53:42 CET 2015
Hi,
Gromacs always calculates full electrostatics at every time step if PME is
used. That means, both the short-range and the long-range Coulomb contribution
of the Ewald sum are updated at every time step.
Carsten
On 19 Jan 2015, at 01:44, asasa qsqs <sanaz_dr_m at yahoo.com> wrote:
> 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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> End of gromacs.org_gmx-users Digest, Vol 129, Issue 63
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa
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