[gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 91
Elias Santos
silvasantosster at gmail.com
Mon Nov 26 16:04:34 CET 2018
Dear Justin,
Thanks for answer.
On Mon, Nov 26, 2018 at 1:01 PM <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: free binding energy calculation (Justin Lemkul)
> 2. Re: sort_mol2_bonds.pl issues (Justin Lemkul)
> 3. Re: Mismatch between gromacs and python-networkx versions
> (Justin Lemkul)
> 4. Re: Charge system simulation problem (Justin Lemkul)
> 5. Re: pH Replica Exchange (Justin Lemkul)
> 6. Re: ionize flag (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 26 Nov 2018 09:55:30 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] free binding energy calculation
> Message-ID: <327a86c6-3e7d-1bc3-931b-addacd3b7f9b at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/23/18 4:07 PM, marzieh dehghan wrote:
> > Thanks a lot for your kind answer, I used the same link to calculate free
> > binding energy and confront the mentioned error.
>
> Please make sure to use a correct subject, and don't reply to the entire
> digest. If you're actively asking/answering questions, I suggest
> subscribing in individual message mode, not digest.
>
> To the original question, if you follow the tutorial and use the files
> at the correct link (mdtutorials.com/gmx), you cannot possibly get the
> error you mentioned before. The old tutorials on the
> bevanlab.biochem.vt.edu site should not be used any more. They are
> outdated and should go offline soon, anyway. The input files on
> mdtutorials.com/gmx are updated and correct for version 2018. You will
> not get the same error.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 26 Nov 2018 09:56:20 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] sort_mol2_bonds.pl issues
> Message-ID: <6da7eec2-e98f-eb26-0db8-de912e285f78 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/26/18 2:46 AM, Francesco Pietra wrote:
> > Hi
> > sort_mol2_bonds.pl (taken from the 2018-updated protein-ligandb
> tutorial)
> > does not work for me. The .mol2 file is simply stripped out of the whole
> > list of bonds, while the atom list remain not ordered (for example oxygen
> > before carbon, or C13 before C1). This occurs with also monotone atom
> > numbering. But I also have cases with also hyphenated due to the presence
> > of side chains. An excerpt from the universal GDP
> > 1 PB 320.9600 448.8530 308.0120 P.3 501 GDP 0.5373
> > 2 O1B 320.2560 449.8240 307.0910 O.3 501 GDP
> -0.1143
> > 3 O2B 320.9220 447.3970 307.6090 O.3 501 GDP
> -0.1143
> > 4 O3B 320.6220 449.1260 309.4600 O.2 501 GDP
> -0.2221
> > 5 O3A 322.5080 449.2690 307.8600 O.3 501 GDP
> -0.2261
> > 6 PA 323.6920 448.5990 308.7260 P.3 501 GDP
> 0.2224
> > 7 O1A 324.3840 447.6240 307.8010 O.3 501 GDP
> -0.4370
> > 8 O2A 323.1200 447.9850 309.9830 O.2 501 GDP
> -0.5170
> > 9 O5' 324.6580 449.8470 309.1210 O.3 501 GDP
> -0.3245
> > 10 C5' 326.0610 449.8930 308.8080 C.3 501 GDP
> 0.0836
> > 11 C4' 326.9510 449.9750 310.0480 C.3 501 GDP
> 0.1133
> > 12 O4' 326.8250 448.7650 310.8190 O.3 501 GDP
> -0.3456
> > 13 C3' 328.4210 450.0360 309.6490 C.3 501 GDP
> 0.1135
> >
> > Did not find anything about on Internet.
>
> Please send me your .mol2 file off-list. The script doesn't do anything
> to the atoms, only the bonds, so I can't tell what's going on. As this
> is not a GROMACS problem, please just contact me directly about the issue.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 26 Nov 2018 09:57:06 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Mismatch between gromacs and python-networkx
> versions
> Message-ID: <101207f5-045f-cbcd-5d60-1c1823e61f69 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/25/18 9:10 AM, Francesco Pietra wrote:
> > This is my first post to gromacs, to which I came in the hope that FEP
> > simulations are more efficient than with other engines.
> >
> > I updated debian amd64 from stretch to buster in order to have the said
> > preferred gromacs 2018 (2016 on stretch). Now, to set up the system
> > (protein+ligands) I have networkx2.x, while 1.11.x (which was on stretch)
> > is required. Am I wrong, or there is really such a mismatch?. If so, how
> to
> > turn around? I have only one version of linux.
>
> GROMACS has no NetworkX requirement. If you're talking about the
> cgenff_charmm2gmx.py script, that's different. You need NetworkX 1.11
> for it to work. But that's not a GROMACS issue.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 26 Nov 2018 09:58:10 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Charge system simulation problem
> Message-ID: <de11509c-4a7c-b386-bc91-3e252865c0cc at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/26/18 12:01 AM, Karpurmanjari Kakati wrote:
> > Dear All,
> >
> > My System contains, while doing NVT of the same, I got the following Note
> >
> >
> >
> >
> >
> >
> > *NOTE 1 [file sa.top, line 80]: System has non-zero total charge:
> > 12.936997 Total charge should normally be an integer. See
> > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> > <http://www.gromacs.org/Documentation/Floating_Point_Arithmetic> for
> > discussion on how close it should be to an integer.*
> >
> >
> > This is possibly because of the partial charges in the molecules in the
> > ITP fie.
>
> Something isn't parametrized correctly because you need to have an
> integer charge. Your total charge is not physical.
>
> -Justin
>
> > My doubt is can't I have a system with non zero and a decimal charge
> value.
> >
> >
> > Also I got the following warning:
> >
> >
> >
> >
> >
> >
> > *WARNING 1 [file sa.top, line 80]: You are using Ewald electrostatics
> in a
> > system with net charge. This can lead to severe artifacts, such as ions
> > moving into regions with low dielectric, due to the uniform background
> > charge. We suggest to neutralize your system with counter ions, possibly
> > in combination with a physiological salt concentration.*
> >
> > Can Someone help me with this?
> >
> > Also this :
> >
> >
> >
> >
> >
> >
> >
> > *Velocities were taken from a Maxwell distribution at 300 KRemoving all
> > charge groups because cutoff-scheme=VerletAnalysing residue names:There
> > are: 1 Other residuesThere are: 100000 Water residues*
> >
> >
> > Removing all charge group because the cut off scheme is verlet.
> >
> > If That happens then will it show the behavior I want to see. Or shall I
> > put any other scheme on that ?
> >
> > Please help
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 26 Nov 2018 09:58:46 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] pH Replica Exchange
> Message-ID: <ab4ce5ef-4555-37fc-326a-d0643fe26a8d at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/26/18 4:50 AM, Reza Esmaeeli wrote:
> > I?m considering Replica Exchange MD for different pH values with GROMACS.
> > Any ideas where to start?
> >
> > (In the literature, this is usually done using Amber or CHARMM packages)
>
> Start by using AMBER or CHARMM :)
>
> AFAIK, there is no support for anything like this in GROMACS.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 26 Nov 2018 09:59:14 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] ionize flag
> Message-ID: <95535e8f-4c94-dc4d-40ff-ae2f7975e6d2 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/26/18 8:34 AM, Elias Santos wrote:
> > Hi everyone!!
> > I'm working with a system in gas-phase, where in the first simulation I
> use
> > the command mdrun -deffnm mdall -v. In the second one, it is bombarded
> with
> > X-ray using the -[yes]ionize flag gromacs 4.5.6. However, comparing the
> two
> > simulations I have observed that the values for energies are the same.
> So,
> > there is something wrong.
> > Could you help me!!
>
> That featured was removed a long time ago because it was unmaintained
> and no one was sure if it worked. Likely it simply doesn't work.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> --
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