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

Fri Jan 19 20:11:44 CET 2018

Hi,

If you want to engage in discussion, please change your settings so that
you aren't receiving digests and replying to them, because that means you
make it hard for all to know what you are replying about.

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:
>
> > Send gromacs.org_gmx-users mailing list submissions to
> > gromacs.org_gmx-users at maillist.sys.kth.se
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or, via email, send a message with subject or body 'help' to
> > gromacs.org_gmx-users-request at maillist.sys.kth.se
> >
> > You can reach the person managing the list at
> > gromacs.org_gmx-users-owner at maillist.sys.kth.se
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gromacs.org_gmx-users digest..."
> >
> > 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
>
> * 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.
>