________________________________________
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Sent: Wednesday, May 16, 2012 2:59 PM
To: [email protected]
Subject: gmx-users Digest, Vol 97, Issue 120
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Today's Topics:
1. Re: grompp Unkown bond_atomtype C2 (Justin A. Lemkul)
2. Re: grompp Unkown bond_atomtype C2 (Lara Bunte)
3. Re: grompp Unkown bond_atomtype C2 (Justin A. Lemkul)
4. Re: Wierd results from Umbrella sampling (Justin A. Lemkul)
5. (no subject) (rama david)
6. Re: (no subject) (Justin A. Lemkul)
7. forcefields for lipids (Shima Arasteh)
----------------------------------------------------------------------
Message: 1
Date: Wed, 16 May 2012 07:22:31 -0400
From: "Justin A. Lemkul" <[email protected]>
Subject: Re: [gmx-users] grompp Unkown bond_atomtype C2
To: Lara Bunte <[email protected]>, Discussion list for GROMACS
users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 5/16/12 3:56 AM, Lara Bunte wrote:
> Hi
>
> After:
>
> pdb2gmx -f mymol.pdb -water tip3p
> editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro
>
> genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
>
>
> I typed:
>
>
> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>
>
> where em.mdp is my energy minimization file and I got:
>
> Fatal error:
> Unknown bond_atomtype C2
>
>
> What is here the problem? All atom types should be declared by me, I guess.
>
You're making use of an atom type called "C2" in some bonded interaction, but
such an atom type doesn't exist. You need to define it.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 2
Date: Wed, 16 May 2012 13:05:24 +0100 (BST)
From: Lara Bunte <[email protected]>
Subject: Re: [gmx-users] grompp Unkown bond_atomtype C2
To: "[email protected]" <[email protected]>
Cc: "[email protected]" <[email protected]>
Message-ID:
<[email protected]>
Content-Type: text/plain; charset=iso-8859-1
Hi
in my .rtp file I wrote in the [ atoms ] block
C2?? CN1A??? 0.7481?? 1
but in the atomtypes.atp file I wrote
CN1A??? 12.01100
So I declared it. So what do you mean with "such an atom type doesn't exist"?
Greetings
Lara
----- Urspr?ngliche Message -----
Von: Justin A. Lemkul <[email protected]>
An: Lara Bunte <[email protected]>; Discussion list for GROMACS users
<[email protected]>
CC:
Gesendet: 13:22 Mittwoch, 16.Mai 2012
Betreff: Re: [gmx-users] grompp Unkown bond_atomtype C2
On 5/16/12 3:56 AM, Lara Bunte wrote:
> Hi
>
> After:
>
> pdb2gmx -f mymol.pdb -water tip3p
> editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro
>
> genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
>
>
> I typed:
>
>
> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>
>
> where em.mdp is my energy minimization file and I got:
>
> Fatal error:
> Unknown bond_atomtype C2
>
>
> What is here the problem? All atom types should be declared by me, I guess.
>
You're making use of an atom type called "C2" in some bonded interaction, but
such an atom type doesn't exist.? You need to define it.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 3
Date: Wed, 16 May 2012 08:08:29 -0400
From: "Justin A. Lemkul" <[email protected]>
Subject: Re: [gmx-users] grompp Unkown bond_atomtype C2
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 5/16/12 8:05 AM, Lara Bunte wrote:
> Hi
>
>
> in my .rtp file I wrote in the [ atoms ] block
>
> C2 CN1A 0.7481 1
>
>
> but in the atomtypes.atp file I wrote
>
> CN1A 12.01100
>
>
> So I declared it. So what do you mean with "such an atom type doesn't exist"?
>
Neither of those actions constitutes what you need. Your atom name is C2, while
its type is CN1A. Apparently somewhere in the bonded parameters you've assigned
C2 as a type, which is wrong. You need to be using CN1A if adding a new bonded
parameter. The CN1A atom type already exists in the force field so you don't
need to do anything special.
Note for the future that in order to add a new atom type (if necessary), it
needs to have its parameters listed in ffbonded.itp. Mentioning it in the .rtp
and .atp files does not do much for you; it simply makes that atom type
accessible in the topology, but if it doesn't have parameters assigned, it is
useless.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 4
Date: Wed, 16 May 2012 08:11:49 -0400
From: "Justin A. Lemkul" <[email protected]>
Subject: Re: [gmx-users] Wierd results from Umbrella sampling
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 5/16/12 4:08 AM, Du Jiangfeng (BIOCH) wrote:
> Dear Sir/Madam,
>
> I have performed umbrella pulling and umbrella sampling my protein from a
> DOPC/DOPS membrane. Unfortunately, the results are really bad (Energy curve
> suddenly turns to zero at the last 1 nm) and the histograph does not show any
> overlap. Actually, I did it strictly based on Justin's tutorial, with the
> sample spacing of 0.2 nm.
>
Please note that the exact protocol in the tutorial may or may not be applicable
to all systems. The overall workflow is the same, but details regarding use of
groups, .mdp files, etc may vary.
> Here are some lines from the end of the energy file (The energy should not
> decrease since it was in summation):
>
> Distance(nm) Energy (Kcal/mol) 5.288348 5.705318e+01 5.316250
> 4.881724e+01
> 5.344152 4.022505e+01 5.372054 3.101854e+01 5.399956 2.208200e+01
> 5.427858
> 1.343340e+01 5.455761 4.267619e+00 5.483663 -5.084078e+00 ? minus 5.511565
> -1.486168e+01 ? minus 5.539467 -2.393515e+01 ? minus 5.567369
> -3.343453e+01
> ? minus
>
What energetic term is this? A summation can decrease if the values being added
are all negative.
The energetic term should be binding energy.
Even there are some samples with the negative energies but the energy curve
shouldn't go to zero (I calculated them by hand).
>
> Followings are some lines from the end of histograph file:
>
> Distance(nm) 5.455761 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0
> 0 8 5.483663 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 8 5.511565 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 12
> 5.539467 0 0 0 0 0 0 0 0
> 0 0 0 0 0 0 0 0 0 0
> 4 5.567369 0 0 0 0 0 0 0 0
> 0 0
> 0 0 0 0 0 0 0 0 2
>
>
> I am really depressed because it took me quiet a long time to sampling but it
> seems in vain... I really no idea to find out what went wrong.
>
Nor do we. What is in your .mdp file? How many windows are you using? What is
the total desired length of the reaction coordinate, and what are the initial
and final COM distances that you are restraining? What are your box dimensions?
-Justin
My box dimensions are x: 7.94677 y: 7.94677 z: 13.48094 (nm)
The initial COM of DOPC(lipids) is at z=3.5 nm;
The initial COM of my protein is at z= 6.65nm.
The desired length is 3.6 nm, but it moved 3.4 nm along z-dimension.
So I used 19 windows for 3.4 nm movement (0.17 nm / window)
In pulling.mdp:
dt= 2 fs; nsteps=1 ns; nstxout=10 ps; nstvout=10ps
rlist/rcoulomb/ rvdw= 1.4
Tcoupl= v-rescale; Pcoupl= Parrinello-Rahman
; Pull code
pull = umbrella
pull_geometry = distance ; simple distance increase
pull_dim = N N Y
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = DOPC
pull_group1 = protein
pull_rate1 = 0.0036 ; 0.0036 nm per ps = 3.6 nm per ns
pull_k1 = 1300 ; kJ mol^-1 nm^-2
In umbrella sampling.mdp:
nsteps=9.5 ns; pull_rate1= 0.0; pull_k1= 1000
other parameters are same as pulling.mdp.
Thank you for your help, above are my parameters.
Jiangfeng.
========================================
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 5
Date: Wed, 16 May 2012 18:19:59 +0530
From: rama david <[email protected]>
Subject: [gmx-users] (no subject)
To: Discussion list for GROMACS users <[email protected]>
Message-ID:
<CAD=-syfb_2xts+wmvduqbpngee_v2h4b9yznkdxxe1sdlyd...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi Gromacs Friends,
I plan to simulate protein In Trifluoro Ethanol solvent
using G96 53a6 FF
Please help to define parameters in md.mdp
For water I am using following mdp file ....
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 0.9 ; short-range neighborlist cutoff (in nm)
rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)
vdw-type = Cut-off
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME
For TFE and water mix of different conc , What should be the mdp file
parameter ???
I am using following ones..
Twin range cutt-off for nnonbonded interactions..
Short range cut-off 0.8 and long range 1.4 for both
coulombic and lennard-jones
Short range updates for every 5 step togather with pair
list..
Please give me valuable suggestion ..
Thank you in advance ..
With Best Wishes,
Rama David
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Message: 6
Date: Wed, 16 May 2012 08:55:00 -0400
From: "Justin A. Lemkul" <[email protected]>
Subject: Re: [gmx-users] (no subject)
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 5/16/12 8:49 AM, rama david wrote:
> Hi Gromacs Friends,
>
> I plan to simulate protein In Trifluoro Ethanol solvent
> using G96 53a6 FF
>
> Please help to define parameters in md.mdp
>
> For water I am using following mdp file ....
>
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> ns_type = grid ; search neighboring grid cells
> nstlist = 5 ; 10 fs
> rlist = 0.9 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)
> vdw-type = Cut-off
> rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME
>
>
>
> For TFE and water mix of different conc , What should be the mdp file
> parameter ???
>
> I am using following ones..
>
> Twin range cutt-off for nnonbonded interactions..
> Short range cut-off 0.8 and long range 1.4 for both
> coulombic and lennard-jones
> Short range updates for every 5 step togather with pair
> list..
>
>
> Please give me valuable suggestion ..
>
The settings given in an .mdp file are dependent upon the force field, not the
molecules in the system. So if you have water or water/TFE, the requirements of
the force field are still the same.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 7
Date: Wed, 16 May 2012 05:59:22 -0700 (PDT)
From: Shima Arasteh <[email protected]>
Subject: [gmx-users] forcefields for lipids
To: Discussion list for GROMACS users <[email protected]>
Message-ID:
<[email protected]>
Content-Type: text/plain; charset="iso-8859-1"
Dear gmx users,
Which force fields are suggested for lipids? Except CHARMM, any other
forcefields?
Anybody may suggest me articles in this about?
Thanks in advance
?
Sincerely,
Shima
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