[gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue 85

Mark Abraham mark.j.abraham at gmail.com
Fri Jan 19 20:11:44 CET 2018


Hi,

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Mark

On Fri, Jan 19, 2018, 20:01 banijamali_fs <banijamali_fs at ut.ac.ir> wrote:

> On 2018-01-19 16:25, gromacs.org_gmx-users-request at maillist.sys.kth.se
> wrote:
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> > Today's Topics:
> >
> > 1. Re: help with my errors (RAHUL SURESH) (banijamali_fs)
> > 2. Re: help with my errors (RAHUL SURESH) (RAHUL SURESH)
> > 3. Re: help with my errors (RAHUL SURESH) (RAHUL SURESH)
> > 4. Re: help with my errors (RAHUL SURESH) (Justin Lemkul)
> > 5. Re: Rupture force definition (Justin Lemkul)
> > 6. Re: tilt angle for POPC (Justin Lemkul)
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 19 Jan 2018 14:59:07 +0330
> > From: banijamali_fs <banijamali_fs at ut.ac.ir>
> > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: Re: [gmx-users] help with my errors (RAHUL SURESH)
> > Message-ID: <a62a62ace22627fc441f2d1091509a19 at ut.ac.ir>
> > Content-Type: text/plain; charset=US-ASCII
> >
> >> Hi there,
> >>
> >> 1. I'm working on MOF (metal organic framewoks) structures. I'd like to
> >> know that if in our topology file we get a decimal figure for the qtot,
> >> in which step we made a mistake? and how we can rectify this?
> >>
> >> 2.  Another question that I have is that when I want to run this
> >> command, gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr, I
> >> get this error,Too many warnings (1), gmx terminated, I don't now how to
> >> rectify this error.
> >>
> >> I would be very thankful if anyone could help me.
> >>
> >> these are the warning that I mentioned above:
> >> Warning: atom name 57 in topol.top and solv.gro does not match (CU -
> CU2)
> >> Warning: atom name 58 in topol.top and solv.gro does not match (CU -
> CU2)
> >>
> >> WARNING 1 [file topol.top, line 114]:
> >> 2 non-matching atom names
> >> atom names from topol.top will be used
> >> atom names from solv.gro will be ignored
> >>
> >> Fatemeh.
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Fri, 19 Jan 2018 17:39:31 +0530
> > From: RAHUL SURESH <drrahulsuresh at gmail.com>
> > To: gmx-users at gromacs.org
> > Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> > Subject: Re: [gmx-users] help with my errors (RAHUL SURESH)
> > Message-ID:
> > <CAAtfiTtDwMGbFCt9pwRdwyQYCxNFbJ-qZPZWwaEANvZOMWh9QQ at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > On Fri, Jan 19, 2018 at 4:59 PM, banijamali_fs <banijamali_fs at ut.ac.ir>
> > wrote:
> >
> > Hi there,
> >
> > 1. I'm working on MOF (metal organic framewoks) structures. I'd like to
> > know that if in our topology file we get a decimal figure for the qtot,
> > in which step we made a mistake? and how we can rectify this?
>
> qtot defines the charge and that can be neutralized in the genion step.
> I
> am not sure if it works different for MOF
>
> >> 2.  Another question that I have is that when I want to run this
> >> command, gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr, I
> >> get this error,Too many warnings (1), gmx terminated, I don't now how to
> >> rectify this error.
> >>
> >> I would be very thankful if anyone could help me.
> >>
> >> these are the warning that I mentioned above:
> >> Warning: atom name 57 in topol.top and solv.gro does not match (CU -
> CU2)
> >> Warning: atom name 58 in topol.top and solv.gro does not match (CU -
> CU2)
> >>
> >> WARNING 1 [file topol.top, line 114]:
> >> 2 non-matching atom names
> >> atom names from topol.top will be used
> >> atom names from solv.gro will be ignored
>
> You can change the name  as in top. so the 2nd error can be eliminated.
>
> >> Fatemeh.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>
> ------------------------------
>
> Message: 3
> Date: Fri, 19 Jan 2018 17:39:31 +0530
> From: RAHUL SURESH <drrahulsuresh at gmail.com>
> To: gmx-users at gromacs.org
> Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] help with my errors (RAHUL SURESH)
> Message-ID:
>     <CAAtfiTtDwMGbFCt9pwRdwyQYCxNFbJ-qZPZWwaEANvZOMWh9QQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> On Fri, Jan 19, 2018 at 4:59 PM, banijamali_fs <banijamali_fs at ut.ac.ir>
> wrote:
>
> >> Hi there,
> >>
> >> 1. I'm working on MOF (metal organic framewoks) structures. I'd like to
> >> know that if in our topology file we get a decimal figure for the qtot,
> >> in which step we made a mistake? and how we can rectify this?
>
> qtot defines the charge and that can be neutralized in the genion step.
> I
> am not sure if it works different for MOF
>
> >> 2.  Another question that I have is that when I want to run this
> >> command, gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr, I
> >> get this error,Too many warnings (1), gmx terminated, I don't now how to
> >> rectify this error.
> >>
> >> I would be very thankful if anyone could help me.
> >>
> >> these are the warning that I mentioned above:
> >> Warning: atom name 57 in topol.top and solv.gro does not match (CU -
> CU2)
> >> Warning: atom name 58 in topol.top and solv.gro does not match (CU -
> CU2)
> >>
> >> WARNING 1 [file topol.top, line 114]:
> >> 2 non-matching atom names
> >> atom names from topol.top will be used
> >> atom names from solv.gro will be ignored
>
> You can change the name  as in top. so the 2nd error can be eliminated.
>
> I didn't understand your recommend. could you hear me please?
> the pdb file of my structure is made of 4 identical ligand. because as
> you know the pdb2gmx command doesn't support metals.so with this
> command,
>
> gmx pdb2gmx -f  LIG.pdb -o  LIG.gro -water spc
>
> LIG.gro will be produced. to have the final gro file of the MOF, I added
>  the coordinate of
>  metals to  LIG.gro file to have MOF.gro file.
> so according to my explain there isn't any CU in topol.top file, because
> topol.top is the product
> of gmx pdb2gmx command that there was't any CU in the LIG.pdb structure,
> after forming LIG.gro
> we add the coordinete of 2 CU into the LIG.gro file and rename it to
> MOF.gro.
>
> could you please help me?
>
> >> Fatemeh.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>
> ------------------------------
>
> Message: 4
> Date: Fri, 19 Jan 2018 07:50:54 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] help with my errors (RAHUL SURESH)
> Message-ID: <da668e2e-1d47-e450-e5f7-309d5ce03e46 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> On 1/19/18 7:09 AM, RAHUL SURESH wrote:
>
> > On Fri, Jan 19, 2018 at 4:59 PM, banijamali_fs <banijamali_fs at ut.ac.ir>
> > wrote:
> >
> > Hi there,
> >
> > 1. I'm working on MOF (metal organic framewoks) structures. I'd like to
> > know that if in our topology file we get a decimal figure for the qtot,
> > in which step we made a mistake? and how we can rectify this?
>  qtot defines the charge and that can be neutralized in the genion step.
> I
> am not sure if it works different for MOF
> No sane species can have a fractional total charge. Is it possible for a
>
> molecule to have part of an electron? Of course not. Any topology that
> sums to a non-integer charge is flawed and needs to be corrected.
> -Justin
>
> yes, you are right, but how can I correct the charges? could you please
> explain it more?
> another question that I have is that why the charges are non-integer, in
> which step I made mistake?
>
> > 2.  Another question that I have is that when I want to run this
> > command, gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr, I
> > get this error,Too many warnings (1), gmx terminated, I don't now how to
> > rectify this error.
> >
> > I would be very thankful if anyone could help me.
> >
> > these are the warning that I mentioned above:
> > Warning: atom name 57 in topol.top and solv.gro does not match (CU - CU2)
> > Warning: atom name 58 in topol.top and solv.gro does not match (CU - CU2)
> >
> > WARNING 1 [file topol.top, line 114]:
> > 2 non-matching atom names
> > atom names from topol.top will be used
> > atom names from solv.gro will be ignored
>  You can change the name  as in top. so the 2nd error can be eliminated.
>
> >> Fatemeh.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> ------------------------------
>
> Message: 5
> Date: Fri, 19 Jan 2018 07:52:38 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Rupture force definition
> Message-ID: <a1ec0a78-84a2-a254-f7b8-96e8d42c5219 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> On 1/19/18 12:52 AM, Rakesh Mishra wrote:
>
> > Dear Justin
> >
> > Thanks for your explanation . Yes I am agree that it will depend on the k
> > value and path direction.
> > Let suppose we map the experimental spring constant and rate then it will
> > be some how relevant for my study.
> >
> > My another query is the same from umbrella sampling of puling code.
> > If I restrain some different molecule (let C ) and give the reference
> > molecule (let B) and pulling molecule (Let A), then
> > I found that , when I pull molecule A in + x direction then C has
> > immobility while  molecule B is feeling opposite force w. r.  t.
> molecule
> > A. i. e. if  molecule A is moving
> > along + x direction then reference molecule B starts to move in - x
> > direction.
> > Now I want to know that in pulling code, does reference molecule and
> > pulling molecule connected with imaginary spring, due  to this newton
> third
> > law is applying here.
>
> Yes, of course. The biasing potential is applied to both species
> specified in the group setup; we use a convention of "pulled" and
> "reference" group for defining a suitable reaction coordinate, but the
> forces are always applied to any group involved in this process.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> ------------------------------
>
> Message: 6
> Date: Fri, 19 Jan 2018 07:55:00 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] tilt angle for POPC
> Message-ID: <d102920b-0d79-f197-a99a-0cffd88d7914 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> On 1/18/18 1:28 PM, Mohsen Ramezanpour wrote:
>
> > Hi Justin,
> >
> > On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote:
> >
> > Dear Gromacs users,
> >
> > I am interested in calculation of tilt angle for the POPC headgroup
> (angle
> > distribution between the P-N vector and Z axis).
> > I am not sure if my approach is correct as my angle distribution does not
> > seem reasonable.
> >
> > Given a bilayer with 200 lipids (100 lipids in each leaflet with
> > resides 1-100 and 101-200 for upper and lower leaflets, respectively)
> > simulated for 200 ns:
> >
> > gmx make_ndx -f SYSTEM.gro  -o index.ndx
> > keep 0
> > r 1-100
> > name 1 upperleaflet
> > 1 & a P
> > 1 & a N
> > 2 | 3
> > name 4 vector
> > q
> >
> > Next, I use:
> > gmx gangle  -f  md.xtc  -s  md.tpr  -n  index.ndx  -g1  vector  -g2  z
> > -b
> > 100000   -group1  -oh histogram.xvg   -binw  0.01
> >
> > and choose index group 4 and then Ctrl+D.
> >
> > Please let me know your opinion. I think I am doing something wrong,
> > especially with the construction of P-N vector.
> >
> > What results do you get from this approach?
>  A normal distribution centered around 105 with a high pick standing out
> around 90.
> I expected it to be around ~73-77
> Upon what are you basing your expectation? Previous literature? Some
> other calculation or visual inspection?
>
> >> What happens if you try to analyze only a single lipid?
> > I get an approximate normal distribution centered around 100 degrees.
> >
> > I have two systems, one is salt free and the other one has 0.15 M NaCL
> salt.
> > The shape of histograms is the same.
> >
> > I had to separate the leaflets, right?
>
> If the membrane is homogeneous, I don't see any reason why.
>
> -Justin
>
> > So, any idea why this is happening?
> >
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Virginia Tech Department of Biochemistry
> >>
> >> 303 Engel Hall
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >>
> >> ==================================================
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/Support
> >> /Mailing_Lists/GMX-Users_List before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> ------------------------------
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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