<div class="gmail_quote"><div>Dear Justin</div><div>Thank you very much for your reply</div><div>>>Regarding Warning 1; Yes, I have introduced the new parameter for C C bond and it is what I want. </div><div>>>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?</div>
<div>>>May I know whether my mdp file contents (rlis, rcoulomb,vdwtype and rvdw) are correct? </div><div>Thanks so much</div><div>M.V.K</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Message: 3<br>
Date: Sat, 20 Aug 2011 17:37:07 -0400<br>
From: "Justin A. Lemkul" <<a 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 href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a 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 Cisplatin<br>
> molecules (198atoms) =1458atoms. I have created the topology 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 SWCNT-DDP-box.pdb -p<br>
> SWCNT-DDP2.top -o SWCNT-DDP2.tpr -maxwarn 5 , However a wrong 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 overriding warnings<br>
that grompp is producing, they typically only occur if the system 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 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 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 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, Then how<br>
> to solve it?<br>
<br>
You have different bonded parameters assigned for a single bond type. You<br>
should investigate why you've produced different parameters for the same<br>
interaction and correct it, if necessary. If you are trying to override<br>
existing parameters, this may be what you want. Otherwise, eliminate the<br>
duplicate entry such that the parameters you actually wish to use are being<br>
assigned.</blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
> 2) Regarding Note 1, Is it necessary to do ionization to make the system<br>
> neutralize before minimization?<br>
<br>
Not in this case. You have a non-integer charge of sufficiently disturbing<br>
magnitude (i.e., it does not arise simply due to floating point 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 it is<br>
> because of using a computer with small processor. Actually I 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 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 href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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<br></blockquote></div>