[gmx-users] RE: Re: Wierd results from Umbrella sampling (Justin A. Lemkul)

Du Jiangfeng (BIOCH) j.du at maastrichtuniversity.nl
Tue May 22 09:36:45 CEST 2012


Dear Justin,

Based on your questions to my simulation, I posted here yesterday hopefully it was the correct way to reply in this forum.

In this morning I got a list of new windows of umbrella sampling, the overlap is sufficient enough, but I saw another problem:  In the histogram figure, the base of peak covers the distance of 2 nm instead of 0.2 nm., that's horrible! However, when I checked back to the simulation results of each window, the fluctuation of my pulled protein is only 0.4nm in maximum. So the base of peak shouldn't cover such long distance, right?

Thank you very much,

Jiangfeng. 

    Jiangfeng Du, PhD Student
    Cardiovascular Research Institute Maastricht
    Department of Biochemistry
    P.O. Box 616
    Mobile: +31-681741859
    FAX: +31-43-3884159
    6200 MD Maastricht
    The Netherlands
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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" <jalemkul at vt.edu>
Subject: Re: [gmx-users] grompp Unkown bond_atomtype C2
To: Lara Bunte <lara.bunte at yahoo.de>,   Discussion list for GROMACS
        users <gmx-users at gromacs.org>
Message-ID: <4FB38DF7.2060804 at vt.edu>
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 <lara.bunte at yahoo.de>
Subject: Re: [gmx-users] grompp Unkown bond_atomtype C2
To: "jalemkul at vt.edu" <jalemkul at vt.edu>
Cc: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Message-ID:
        <1337169924.86371.YahooMailNeo at web29405.mail.ird.yahoo.com>
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 <jalemkul at vt.edu>
An: Lara Bunte <lara.bunte at yahoo.de>; Discussion list for GROMACS users <gmx-users at gromacs.org>
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" <jalemkul at vt.edu>
Subject: Re: [gmx-users] grompp Unkown bond_atomtype C2
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4FB398BD.6010105 at vt.edu>
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" <jalemkul at vt.edu>
Subject: Re: [gmx-users] Wierd results from Umbrella sampling
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4FB39985.9000307 at vt.edu>
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.

>
> 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

--
========================================

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 <ramadavidgroup at gmail.com>
Subject: [gmx-users] (no subject)
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
        <CAD=-SYFb_2xtS+WMVdUQBpngEe_V2H4b9YZNkdXXE1SDLydUWw at 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" <jalemkul at vt.edu>
Subject: Re: [gmx-users] (no subject)
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4FB3A3A4.4060002 at vt.edu>
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 <shima_arasteh2001 at yahoo.com>
Subject: [gmx-users] forcefields for lipids
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
        <1337173162.97860.YahooMailNeo at web36403.mail.mud.yahoo.com>
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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