Re: [gmx-users] gmx-users Digest, Vol 88, Issue 131

[Mark Abraham]

;
> > After entering the command; grompp -f mdmin1.mdp -c
> SWCNT-DDP-box.pdb -p
> > SWCNT-DDP2.top -o SWCNT-DDP2.tpr -maxwarn 5 , However a wrong
> TPR file
> > is generated, I also get 2 notes and 1 warning as stated below;
>
> The -maxwarn option should almost never be used.  If you're
> overriding warnings
> that grompp is producing, they typically only occur if the
system
> will become
> unstable.  Beware.
>
> > WARNING 1 [file ffbonded.itp, line 2705]:
> >   Overriding Bond parameters.
> >
> >   old: 0.151 292880 0.151 292880
> >   new: CC1 0.14210   478900
> >
> > Generated 347361 of the 347361 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 0.5
> > Generated 347361 of the 347361 1-4 parameter combinations
> > Excluding 3 bonded neighbours molecule type 'ICE'
> >
> > NOTE 1 [file SWCNT-DDP2.top, line 15383]:
> >   System has non-zero total charge: -3.097796e-01
> >
> >
> >
> > Analysing residue names:
> > There are: 2  Other residues
> > Analysing residues not classified as Protein/DNA/RNA/Water and
> splitting
> > into groups...
> > Number of degrees of freedom in T-Coupling group rest is 4371.00
> > Calculating fourier grid dimensions for X Y Z
> > Using a fourier grid of 120x120x120, spacing 0.118 0.118 0.118
> > Estimate for the relative computational load of the PME mesh
> part: 0.97
> >
> > NOTE 2 [file mdmin1.mdp]:
> >   The optimal PME mesh load for parallel simulations is below 0.5
> >   and for highly parallel simulations between 0.25 and 0.33,
> >   for higher performance, increase the cut-off and the PME grid
> spacing
> >
> > This run will generate roughly 0 Mb of data.
> >
> > My questions:
> > 1) May I know whether warning 1 should be taken serious?If yes,
> Then how
> > to solve it?
>
> You have different bonded parameters assigned for a single bond
> type.  You
> should investigate why you've produced different parameters for
> the same
> interaction and correct it, if necessary.  If you are trying to
> override
> existing parameters, this may be what you want.  Otherwise,
> eliminate the
> duplicate entry such that the parameters you actually wish
to use
> are being
> assigned.
>
>
> > 2) Regarding Note 1, Is it necessary to do ionization to make
> the system
> > neutralize before minimization?
>
> Not in this case.  You have a non-integer charge of sufficiently
> disturbing
> magnitude (i.e., it does not arise simply due to floating point
> arithmetic),
> indicating that the charges assigned in the topology are junk.
>
> > 3) Regarding Note 2, Is there anything wrong with my mdp file or
> it is
> > because of using a computer with small processor. Actually I
> just tried
> > to do this minimization on my laptop for the first time. If the
> > processor is too small for this calculation, I may be able to
> work with
> > our cluster if it is advised.
>
> For minimization, this often happens.  It is unimportant in
this case.
    >
    > -Justin
>
> >
> > Thank you very much
> > Best regards
> > M.V.K
> >
> >
> >
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080 
> 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
>
>

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[gmx-users] gmx-users Digest, Vol 88, Issue 131

[meisam valizadeh kiamahalleh]

; > > WARNING 1 [file ffbonded.itp, line 2705]:
> > >   Overriding Bond parameters.
> > >
> > >   old: 0.151 292880 0.151 292880
> > >   new: CC1 0.14210   478900
> > >
> > > Generated 347361 of the 347361 non-bonded parameter combinations
> > > Generating 1-4 interactions: fudge = 0.5
> > > Generated 347361 of the 347361 1-4 parameter combinations
> > > Excluding 3 bonded neighbours molecule type 'ICE'
> > >
> > > NOTE 1 [file SWCNT-DDP2.top, line 15383]:
> > >   System has non-zero total charge: -3.097796e-01
> > >
> > >
> > >
> > > Analysing residue names:
> > > There are: 2  Other residues
> > > Analysing residues not classified as Protein/DNA/RNA/Water and
> > splitting
> > > into groups...
> > > Number of degrees of freedom in T-Coupling group rest is 4371.00
> > > Calculating fourier grid dimensions for X Y Z
> > > Using a fourier grid of 120x120x120, spacing 0.118 0.118 0.118
> > > Estimate for the relative computational load of the PME mesh
> > part: 0.97
> > >
> > > NOTE 2 [file mdmin1.mdp]:
> > >   The optimal PME mesh load for parallel simulations is below 0.5
> > >   and for highly parallel simulations between 0.25 and 0.33,
> > >   for higher performance, increase the cut-off and the PME grid
> > spacing
> > >
> > > This run will generate roughly 0 Mb of data.
> > >
> > > My questions:
> > > 1) May I know whether warning 1 should be taken serious?If yes,
> > Then how
> > > to solve it?
> >
> > You have different bonded parameters assigned for a single bond
> > type.  You
> > should investigate why you've produced different parameters for
> > the same
> > interaction and correct it, if necessary.  If you are trying to
> > override
> > existing parameters, this may be what you want.  Otherwise,
> > eliminate the
> > duplicate entry such that the parameters you actually wish to use
> > are being
> > assigned.
> >
> >
> > > 2) Regarding Note 1, Is it necessary to do ionization to make
> > the system
> > > neutralize before minimization?
> >
> > Not in this case.  You have a non-integer charge of sufficiently
> > disturbing
> > magnitude (i.e., it does not arise simply due to floating point
> > arithmetic),
> > indicating that the charges assigned in the topology are junk.
> >
> > > 3) Regarding Note 2, Is there anything wrong with my mdp file or
> > it is
> > > because of using a computer with small processor. Actually I
> > just tried
> > > to do this minimization on my laptop for the first time. If the
> > > processor is too small for this calculation, I may be able to
> > work with
> > > our cluster if it is advised.
> >
> > For minimization, this often happens.  It is unimportant in this
> case.
> >
> > -Justin
> >
> > >
> > > Thank you very much
> > > Best regards
> > > M.V.K
> > >
> > >
> > >
> >
> > --
> > 
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> > 
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > 
> >
> >
> >
>
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Re: [gmx-users] Re: Re：the mdp parameters for lo calpressure calculation using gromacs-4.0.2_localpressure

[wibke . sudholt]

Dear Email Sender,

Thank you very much for contacting me! Unfortunately, I am not available in the 
office at the moment and cannot respond to your email. I will be able to handle 
your request starting again Monday, August 22, 2011.

For all questions about CloudBroker and the CloudBroker Platform, please 
contact the company under i...@cloudbroker.com or Nicola Fantini under 
nicola.fant...@cloudbroker.com. If you need to talk to me in person for urgent 
or important issues, please call my mobile phone number.

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[gmx-users] Re: Re：the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure

[Jianguo Li]

From: KONG Xian 
To: ljg...@yahoo.com.sg
Cc: gmx-users@gromacs.org
Sent: Sunday, 21 August 2011 19:20:50
Subject: Re：the mdp parameters for localpressure calculation using 
gromacs-4.0.2_localpressure

 
Thanks for your kindly reply. 
I used the LINCS calculated the pressure field. The distinct between protein 
and 
the lipid bilayer is obvious from the pressure field. 

But the lipid bilayer and the water is not very obvious , they seems to be a 
uniform from the pressure field calculated. As in Ollila’s original paper: 3D 
Pressure Field in Lipid Membranes and Membrane-Protein Complexes, there is an 
distinct separation region between membrane and the water.
Maybe the LINCS is the problem.
Another problem is perhaps the localpressure software is for CG model? My model 
is all-atom model and the simulation time length is not long enough, maybe this 
is the cause of the results? 

-- From my limited experience, the local pressure calculation converges  very 
poorly. It takes more than 50 ns of production run in my case  to get a 
converged profile. You can divide the production run into several  
sub-trajectories to judge the convergence.

KONG Xian
2011/8/21
 
Hi, Kong Xian,
 
It is better to use SHAKE instead of LINCS since LINCS does not directly yield 
pairwise forces, as shown in the paper: Erik Lindahl and Olle Edholm. Spatial 
and energetic-entropic decomposition of surface tension in lipid bilayers from 
molecular dynamics simulations. JOURNAL OF CHEMICAL PHYSICS, VOLUME 113, NUMBER 
9, 3882b3893.
 
best regards,
Jianguo 
 
 
 
 

From: KONG Xian 
To: gmx-users@gromacs.org
Sent: Friday, 19 August 2011 23:50:01
Subject: [gmx-users] the mdp parameters for localpressure calculation using 
gromacs-4.0.2_localpressure
 
I have sent this email days ago, but I got no answer.
Hope someone would saw it this time. 
Sorry for disturbing.
Dear all:
 I am using gromacs-4.0.2_localpressure to calculate the local pressure 
of my system.
 I have a question.
 When rerun the mdrun from gromacs-4.0.2_localpressure I used a new 
.mdp 
file. There are some changes of the new .mdp file according the original one. I 
have 2 questions:
1.  I changed the The coulomb interaction type from PME to reaction field 
with epsilon_r=1 epsilon_rf=78;  Is this change feasible?
2.  I used LINCS for all bonds in the simulation, and I still use the LINCS 
for all bonds when calculate the local pressure. Is this way right? 
 
Thanks for any reply.
Best wishes,
KONG Xian
Tsinghua, Beijing, China
 
 

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Re: [gmx-users] FEP charged molecule cuestion

[David Mobley]

This is a tough issue and there are some unresolved questions here.

I recommend seeing the work of Kastenholz and Hunenberger on ion solvation
in JCP a couple years ago (two companion papers) as these explain the key
issues.

Thanks.

On Wed, Aug 17, 2011 at 3:24 AM, Marcelino Arciniega Castro <
macas...@mytum.de> wrote:

> Hi there,
>
> Could someone please share some ideas about the next situation?:
>
> I am trying to estimate the relative binding affinity of two small
> molecules to a protein. In the setup process, ions are added in the solvent
> to neutralize the system. Then as everybody suggest, the ligand partial
> charges should be decouple to zero. But my specific case, the small
> molecules are charged, that means that after turning off the ligand partial
> charges, the system will have a net charge (because the ions in the
> solvent). Turning off the ions charges does not solve the problem, because
> of the protein charges.
>
> The concrete question are:
> Should I continue to atom mutation step using PME in a non-neutral system?
> It would make sense to turn off the partial charges of the some atoms in
> the small molecule (just those that are going to be mutated)?
>
> Thanks in advance
> Marcelino
> --
> gmx-users mailing listgmx-users@gromacs.org
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-- 
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dmob...@gmail.com
504-383-3662
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Re: [gmx-users] Re: Warning and Notes in Grompp for minimization

[Mark Abraham]

On 21/08/2011 4:42 PM, meisam valizadeh kiamahalleh wrote:

Dear Justin
Thank you very much for your reply
>>Regarding Warning 1; Yes, I have introduced the new parameter for C 
C bond and it is what I want.
>>Regarding Note 1;  Actually, the charges for each atom in topology 
file are what I included myself in Cisplatin parameters based on 
the literature. May I know what should I do if I have non-integer 
charge in this case?


Each molecule has to have an integer for its total charge. You'll need 
to investigate in your .top file why this is not the case.


>>May I know whether my mdp file contents (rlis, rcoulomb,vdwtype 
and rvdw) are correct?


They're not evidently wrong, but you need to choose these kinds of 
parameters to be consistent with the force field you are using. If 
someone's parametrized cis-platin with a carbon nanotube, then you have 
simply to copy what they did. If not, then you are very likely to 
struggle to get something working that proves to be a valid model - and 
very much more so if this happens to be your first excursion into MD 
simulations. See 
http://www.gromacs.org/Documentation/How-tos/Parameterization


Mark


Thanks so much
M.V.K

Message: 3
Date: Sat, 20 Aug 2011 17:37:07 -0400
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] Warning and Notes in Grompp for minimization
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID: <4e502903.6010...@vt.edu >
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



meisam valizadeh kiamahalleh wrote:
> Dear gmx-users
> Good day to you
> I have a system including carbon nanotube (1260atoms) and 18
Cisplatin
> molecules (198atoms) =1458atoms. I have created the topology
file of the
> system and now I would like to run minimization on this system.
> The content of my mdp file is as below;
>
> define   = -DFLEXIBLE
> constraints  = none
> integrator   = steep
> dt   = 0.002 ; ps !
> nsteps   = 400
> nstlist  = 10
> ns_type  = grid
> rlist= 1
> coulombtype  = PME
> rcoulomb = 1
> vdwtype  = cut-off
> rvdw = 1.4
> optimize_fft = yes
> ;
> ;Energy minimizing stuff
> ;
> emtol= 1000.0
> emstep   = 0.01
>
> After entering the command; grompp -f mdmin1.mdp -c
SWCNT-DDP-box.pdb -p
> SWCNT-DDP2.top -o SWCNT-DDP2.tpr -maxwarn 5 , However a wrong
TPR file
> is generated, I also get 2 notes and 1 warning as stated below;

The -maxwarn option should almost never be used.  If you're
overriding warnings
that grompp is producing, they typically only occur if the system
will become
unstable.  Beware.

> WARNING 1 [file ffbonded.itp, line 2705]:
>   Overriding Bond parameters.
>
>   old: 0.151 292880 0.151 292880
>   new: CC1 0.14210   478900
>
> Generated 347361 of the 347361 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 347361 of the 347361 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'ICE'
>
> NOTE 1 [file SWCNT-DDP2.top, line 15383]:
>   System has non-zero total charge: -3.097796e-01
>
>
>
> Analysing residue names:
> There are: 2  Other residues
> Analysing residues not classified as Protein/DNA/RNA/Water and
splitting
> into groups...
> Number of degrees of freedom in T-Coupling group rest is 4371.00
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 120x120x120, spacing 0.118 0.118 0.118
> Estimate for the relative computational load of the PME mesh
part: 0.97
>
> NOTE 2 [file mdmin1.mdp]:
>   The optimal PME mesh load for parallel simulations is below 0.5
>   and for highly parallel simulations between 0.25 and 0.33,
>   for higher performance, increase the cut-off and the PME grid
spacing
>
> This run will generate roughly 0 Mb of data.
>
> My questions:
> 1) May I know whether warning 1 should be taken serious?If yes,
Then how
> to solve it?

You have different bonded parameters assigned for a single bond
type.  You
should investigate why you've produced different parameters for
the same
interaction and correct it, if necessary.  If you are trying to
override
existing parameters, this may be what you want.  Otherwise,
eliminate the
duplicate entry such that the parameters you actually wish to use
are being
assigned.


> 2) Regarding Note 1, Is it necessary to do ionization to make
the system
> neutralize before minimization?

Not in this case.