<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 22/08/2011 4:50 PM, meisam valizadeh kiamahalleh wrote:
<blockquote
cite="mid:CAOh12OFSTUV23VVjCmgf9LfDVbtUZy0U+TO0OauW6Own1YTxag@mail.gmail.com"
type="cite"><br>
Dear Mark<br>
Thank you very much for your kind reply and advice. <br>
Actually I have the parameters for cisplatin and carbon nanotubes.
and I have generated all forcefield parameter properly. there is
no mis-matching. I have solved the non-integer charge problem by
modifying the topology file manually as far as I had the charges
value from literature.<br>
But I still have one note which stop the calculation of
minimization. </blockquote>
<br>
Notes do not stop correct completion - they bring matters to your
attention that you may wish to address.<br>
<br>
<blockquote
cite="mid:CAOh12OFSTUV23VVjCmgf9LfDVbtUZy0U+TO0OauW6Own1YTxag@mail.gmail.com"
type="cite">The note is as stated below. Kindly would you please
help me on how to solve this matter?<br>
<br>
<span style="color: rgb(255, 0, 0);">NOTE 1 [file mdmin1.mdp]:</span><br
style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);"> The optimal PME mesh load
for parallel simulations is below 0.5</span><br style="color:
rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);"> and for highly parallel
simulations between 0.25 and 0.33,</span><br style="color:
rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);"> for higher performance,
increase the cut-off and the PME grid spacing</span><br
style="color: rgb(255, 0, 0);">
</blockquote>
<br>
Justin addressed this issue in his email several days ago. It is a
useful advisory message about possible inefficiency, but irrelevant
for a calculation whose length will be measured in seconds.<br>
<br>
<blockquote
cite="mid:CAOh12OFSTUV23VVjCmgf9LfDVbtUZy0U+TO0OauW6Own1YTxag@mail.gmail.com"
type="cite"><br style="color: rgb(255, 0, 0);">
<span style="color: rgb(255, 0, 0);">This run will generate
roughly 0 Mb of data</span><br>
</blockquote>
<br>
Advisory message only.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAOh12OFSTUV23VVjCmgf9LfDVbtUZy0U+TO0OauW6Own1YTxag@mail.gmail.com"
type="cite">
<br>
<br>
Thank you very much<br>
Meisam<br>
<br>
<br>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="border-left: 1px solid
rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left:
1ex;">
Message: 1<br>
Date: Sun, 21 Aug 2011 17:32:35 +1000<br>
From: Mark Abraham <<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Re: Warning and Notes in Grompp for<br>
minimization<br>
To: Discussion list for GROMACS users <<a
moz-do-not-send="true" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a moz-do-not-send="true"
href="mailto:4E50B493.3050508@anu.edu.au">4E50B493.3050508@anu.edu.au</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On 21/08/2011 4:42 PM, meisam valizadeh kiamahalleh wrote:<br>
> Dear Justin<br>
> Thank you very much for your reply<br>
> >>Regarding Warning 1; Yes, I have introduced the
new parameter for C<br>
> C bond and it is what I want.<br>
> >>Regarding Note 1; Actually, the charges for each
atom in topology<br>
> file are what I included myself in Cisplatin parameters
based on<br>
> the literature. May I know what should I do if I have
non-integer<br>
> charge in this case?<br>
<br>
Each molecule has to have an integer for its total charge.
You'll need<br>
to investigate in your .top file why this is not the case.<br>
<br>
> >>May I know whether my mdp file contents (rlis,
rcoulomb,vdwtype<br>
> and rvdw) are correct?<br>
<br>
They're not evidently wrong, but you need to choose these
kinds of<br>
parameters to be consistent with the force field you are
using. If<br>
someone's parametrized cis-platin with a carbon nanotube, then
you have<br>
simply to copy what they did. If not, then you are very likely
to<br>
struggle to get something working that proves to be a valid
model - and<br>
very much more so if this happens to be your first excursion
into MD<br>
simulations. See<br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Parameterization"
target="_blank">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><br>
<br>
Mark<br>
<br>
> Thanks so much<br>
> M.V.K<br>
><br>
> Message: 3<br>
> Date: Sat, 20 Aug 2011 17:37:07 -0400<br>
> From: "Justin A. Lemkul" <<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>
<mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>><br>
> Subject: Re: [gmx-users] Warning and Notes in Grompp
for minimization<br>
> To: Discussion list for GROMACS users <<a
moz-do-not-send="true" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <mailto:<a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>><br>
> Message-ID: <<a moz-do-not-send="true"
href="mailto:4E502903.6010100@vt.edu">4E502903.6010100@vt.edu</a>
<mailto:<a moz-do-not-send="true"
href="mailto:4E502903.6010100@vt.edu">4E502903.6010100@vt.edu</a>>><br>
> Content-Type: text/plain; charset=ISO-8859-1;
format=flowed<br>
><br>
><br>
><br>
> meisam valizadeh kiamahalleh wrote:<br>
> > Dear gmx-users<br>
> > Good day to you<br>
> > I have a system including carbon nanotube
(1260atoms) and 18<br>
> Cisplatin<br>
> > molecules (198atoms) =1458atoms. I have created
the topology<br>
> file of the<br>
> > system and now I would like to run minimization
on this system.<br>
> > The content of my mdp file is as below;<br>
> ><br>
> > define = -DFLEXIBLE<br>
> > constraints = none<br>
> > integrator = steep<br>
> > dt = 0.002 ; ps !<br>
> > nsteps = 400<br>
> > nstlist = 10<br>
> > ns_type = grid<br>
> > rlist = 1<br>
> > coulombtype = PME<br>
> > rcoulomb = 1<br>
> > vdwtype = cut-off<br>
> > rvdw = 1.4<br>
> > optimize_fft = yes<br>
> > ;<br>
> > ; Energy minimizing stuff<br>
> > ;<br>
> > emtol = 1000.0<br>
> > emstep = 0.01<br>
> ><br>
> > After entering the command; grompp -f mdmin1.mdp
-c<br>
> SWCNT-DDP-box.pdb -p<br>
> > SWCNT-DDP2.top -o SWCNT-DDP2.tpr -maxwarn 5 ,
However a wrong<br>
> TPR file<br>
> > is generated, I also get 2 notes and 1 warning
as stated below;<br>
><br>
> The -maxwarn option should almost never be used. If
you're<br>
> overriding warnings<br>
> that grompp is producing, they typically only occur
if the system<br>
> will become<br>
> unstable. Beware.<br>
><br>
> > WARNING 1 [file ffbonded.itp, line 2705]:<br>
> > Overriding Bond parameters.<br>
> ><br>
> > old: 0.151 292880 0.151 292880<br>
> > new: C C 1 0.14210 478900<br>
> ><br>
> > Generated 347361 of the 347361 non-bonded
parameter combinations<br>
> > Generating 1-4 interactions: fudge = 0.5<br>
> > Generated 347361 of the 347361 1-4 parameter
combinations<br>
> > Excluding 3 bonded neighbours molecule type
'ICE'<br>
> ><br>
> > NOTE 1 [file SWCNT-DDP2.top, line 15383]:<br>
> > System has non-zero total charge:
-3.097796e-01<br>
> ><br>
> ><br>
> ><br>
> > Analysing residue names:<br>
> > There are: 2 Other residues<br>
> > Analysing residues not classified as
Protein/DNA/RNA/Water and<br>
> splitting<br>
> > into groups...<br>
> > Number of degrees of freedom in T-Coupling group
rest is 4371.00<br>
> > Calculating fourier grid dimensions for X Y Z<br>
> > Using a fourier grid of 120x120x120, spacing
0.118 0.118 0.118<br>
> > Estimate for the relative computational load of
the PME mesh<br>
> part: 0.97<br>
> ><br>
> > NOTE 2 [file mdmin1.mdp]:<br>
> > The optimal PME mesh load for parallel
simulations is below 0.5<br>
> > and for highly parallel simulations between
0.25 and 0.33,<br>
> > for higher performance, increase the cut-off
and the PME grid<br>
> spacing<br>
> ><br>
> > This run will generate roughly 0 Mb of data.<br>
> ><br>
> > My questions:<br>
> > 1) May I know whether warning 1 should be taken
serious?If yes,<br>
> Then how<br>
> > to solve it?<br>
><br>
> You have different bonded parameters assigned for a
single bond<br>
> type. You<br>
> should investigate why you've produced different
parameters for<br>
> the same<br>
> interaction and correct it, if necessary. If you are
trying to<br>
> override<br>
> existing parameters, this may be what you want.
Otherwise,<br>
> eliminate the<br>
> duplicate entry such that the parameters you actually
wish to use<br>
> are being<br>
> assigned.<br>
><br>
><br>
> > 2) Regarding Note 1, Is it necessary to do
ionization to make<br>
> the system<br>
> > neutralize before minimization?<br>
><br>
> Not in this case. You have a non-integer charge of
sufficiently<br>
> disturbing<br>
> magnitude (i.e., it does not arise simply due to
floating point<br>
> arithmetic),<br>
> indicating that the charges assigned in the topology
are junk.<br>
><br>
> > 3) Regarding Note 2, Is there anything wrong
with my mdp file or<br>
> it is<br>
> > because of using a computer with small
processor. Actually I<br>
> just tried<br>
> > to do this minimization on my laptop for the
first time. If the<br>
> > processor is too small for this calculation, I
may be able to<br>
> work with<br>
> > our cluster if it is advised.<br>
><br>
> For minimization, this often happens. It is
unimportant in this case.<br>
><br>
> -Justin<br>
><br>
> ><br>
> > Thank you very much<br>
> > Best regards<br>
> > M.V.K<br>
> ><br>
> ><br>
> ><br>
><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a moz-do-not-send="true"
href="http://vt.edu" target="_blank">vt.edu</a> <<a
moz-do-not-send="true" href="http://vt.edu" target="_blank">http://vt.edu</a>>
| <a moz-do-not-send="true" href="tel:%28540%29%20231-9080"
value="+15402319080">(540) 231-9080</a><br>
> <tel:%28540%29%20231-9080><br>
> <a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
> ========================================<br>
><br>
><br>
><br>
<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a moz-do-not-send="true"
href="http://lists.gromacs.org/pipermail/gmx-users/attachments/20110821/6ce19dcb/attachment-0001.html"
target="_blank">http://lists.gromacs.org/pipermail/gmx-users/attachments/20110821/6ce19dcb/attachment-0001.html</a><br>
<br>
------------------------------<br>
<font color="#888888"><br>
--<br>
gmx-users mailing list<br>
<a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
<br>
End of gmx-users Digest, Vol 88, Issue 131<br>
******************************************<br>
</font></blockquote>
</div>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>