Re: [gmx-users] virtual site connected to dummy massive site

[Mark Abraham]

Hi,

Your systems have different available degrees of freedom, so they sample
difference spaces. The energies you observe reflect that difference.

Mark

On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh  wrote:

> Hi,
>
> I have a system containing of a virtual site of carbon connected
> symmetrically to two dummy massive sites (no charge). like :  M---C---M
> My problem is the results I get from simulation of this system is not equal
> with results of single Carbon system simulation with mass of 2M (at exactly
> similar conditions)?
> They produce different LJ coul energies, I have even tried for non-charged
> systems.
>
> Thank you in advance for help,
> Best regards
> --
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Re: [gmx-users] Regarding calculating the water orientation profile

[Mark Abraham]

Hi,

"Coming closer" implies you care about distance, but your original question
was about orientation. So it's unclear what you want.

Mark

On Thu, 23 Nov 2017 16:50 Dilip H N  wrote:

> I want to calculate whether the water molecules are coming closer towards
> the N-terminal or towards the C-terminal of the amino-acid throughout  the
> simualtion.
> And hence it can shed some light on the Hydrogen bond
> dynamicshopefully...
>
> Thank you
>
>
>
>  Sent with Mailtrack
> <
> https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality
> >
>
> On Thu, Nov 23, 2017 at 6:05 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > It sounds like to need to be more clear about what you want to calculate
> > before you can sensibly find a tool to do it. You should be able to write
> > down the equation for what you want to compute as your observation long
> > before you run a simulation, or how will you know what data to collect?
> >
> > Mark
> >
> > On Thu, 23 Nov 2017 07:26 Dilip H N  wrote:
> >
> > > Hello Sir,
> > > I have run a simulation of amino-acid (glycine) with water molecules
> for
> > 10
> > > ns. Now i need to find out/analyze that whether the water molecules are
> > > getting/more oriented towards N-terminal of glycine or towards the
> > > C-terminal of glycine. (i hope this is what water orientation profile
> > means
> > > ie., the preferential orientation of water towards particular
> > > moeity/group...).
> > > So, which is the exact module/command to find this..?? wether gmx
> sorient
> > > or gmx gangle or gmx angle ..??
> > >
> > > How to resolve this issue...
> > >
> > > Thank you
> > >
> > >
> > > --
> > > With Best Regards,
> > >
> > > DILIP.H.N
> > > Ph.D Student
> > >
> > >
> > >
> > > ‌
> > >  Sent with Mailtrack
> > > <
> > > https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/
> > ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_
> > medium=signature&utm_campaign=signaturevirality
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
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> > >
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > --
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> > send a mail to gmx-users-requ...@gromacs.org.
>
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
> --
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Re: [gmx-users] Regarding calculating the water orientation profile

[soumadwip ghosh]

Hi Dilip,

Here is what you can do. In my guess, you are trying to calculate the
preferential binding affinity of water for N/C terminal domain of your
protein. You can look up for papers that contain Kirkwood-Buff integrals
and preferential binding coefficients. It basically works in the following
way:

1. Specify some atoms belonging to either N- or C-terminus (say COM or any
specific amino acid of your interest for each) and the OW atoms of SOL in
an index file. Calculate the RDF for OW from each separately. Say these
RDFs are g.n and g.c respectively. Now in the following equation

GN = integration (4*pi*r*r*(g.n-1)*dr) and CN = integration
(4*pi*r*r*(g.c-1)*dr )where . Take the integral value from zero till the
first solvation shell (say 3 angstrom, you can guess it from the RDF
profiles as well). Now calculate GN-CN. If its positive then water
molecules are preferentially bound to the N terminus or vice versa.

Let me know if you get it done. Best of luck!

Soumadwip Ghosh
Post Doctoral Research Associate
City of Hope National Medical Center
Duarte, CA 91010
United States
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Re: [gmx-users] Regarding calculating the water orientation profile

[Dilip H N]

Hi Joao Sir,
Yes, that was me, who had asked the questions some time ago, but i had no
success in this.



 Sent with Mailtrack


On Fri, Nov 24, 2017 at 12:11 AM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> Wait, now I remember, you even approached me in a private message and we
> exchanged quite a few emails. Did you try any of my suggestions? No
> success?
>
> J
>
> On Thu, Nov 23, 2017 at 7:36 PM, João Henriques <
> joao.m.a.henriq...@gmail.com> wrote:
>
> > Hi,
> >
> > I clearly remember replying to something similar sometime ago, and I'm
> > almost sure the post was yours. It may be a good idea to rummage through
> > the mailing list, because I'm pretty sure this type of analysis has been
> > discussed here more than once.
> >
> > Cheers,
> > J
> >
> > On Thu, Nov 23, 2017 at 4:41 PM, Dilip H N 
> > wrote:
> >
> >> I want to calculate whether the water molecules are coming closer
> towards
> >> the N-terminal or towards the C-terminal of the amino-acid throughout
> the
> >> simualtion.
> >> And hence it can shed some light on the Hydrogen bond
> >> dynamicshopefully...
> >>
> >> Thank you
> >>
> >>
> >>
> >>  Sent with Mailtrack
> >>  >> il-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&
> >> utm_medium=signature&utm_campaign=signaturevirality>
> >>
> >> On Thu, Nov 23, 2017 at 6:05 PM, Mark Abraham  >
> >> wrote:
> >>
> >> > Hi,
> >> >
> >> > It sounds like to need to be more clear about what you want to
> calculate
> >> > before you can sensibly find a tool to do it. You should be able to
> >> write
> >> > down the equation for what you want to compute as your observation
> long
> >> > before you run a simulation, or how will you know what data to
> collect?
> >> >
> >> > Mark
> >> >
> >> > On Thu, 23 Nov 2017 07:26 Dilip H N 
> wrote:
> >> >
> >> > > Hello Sir,
> >> > > I have run a simulation of amino-acid (glycine) with water molecules
> >> for
> >> > 10
> >> > > ns. Now i need to find out/analyze that whether the water molecules
> >> are
> >> > > getting/more oriented towards N-terminal of glycine or towards the
> >> > > C-terminal of glycine. (i hope this is what water orientation
> profile
> >> > means
> >> > > ie., the preferential orientation of water towards particular
> >> > > moeity/group...).
> >> > > So, which is the exact module/command to find this..?? wether gmx
> >> sorient
> >> > > or gmx gangle or gmx angle ..??
> >> > >
> >> > > How to resolve this issue...
> >> > >
> >> > > Thank you
> >> > >
> >> > >
> >> > > --
> >> > > With Best Regards,
> >> > >
> >> > > DILIP.H.N
> >> > > Ph.D Student
> >> > >
> >> > >
> >> > >
> >> > > ‌
> >> > >  Sent with Mailtrack
> >> > > <
> >> > > https://chrome.google.com/webstore/detail/mailtrack-for-
> gmail-inbox/
> >> > ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_
> >> > medium=signature&utm_campaign=signaturevirality
> >> > > >
> >> > > --
> >> > > 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-requ...@gromacs.org.
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at http://www.gromacs.org/
> >> > Support/Mailing_Lists/GMX-Users_List before posting!
> >> >
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> >> >
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> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> > send a mail to gmx-users-requ...@gromacs.org.
> >>
> >>
> >>
> >>
> >> --
> >> With Best Regards,
> >>
> >> DILIP.H.N
> >> Ph.D Student
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/Support
> >> /Mailing_Lists/GMX-Users_List before posting!
> >>
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> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> >
> --
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>



-- 
With Best Regards,

DILIP.H.N
Ph

Re: [gmx-users] how to checkpoint per steps

[Justin Lemkul]

On 11/23/17 10:02 PM, Du, Yu wrote:

Dear GMX Users,


In GMX, I can't checkpoint per some MD steps but only checkpoint per wall time 
period, right?


Right.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] how to checkpoint per steps

[Du, Yu]

Dear GMX Users, 


In GMX, I can't checkpoint per some MD steps but only checkpoint per wall time 
period, right?



--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275
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Re: [gmx-users] Does RMSD only consider the "relative" coordinate changes for the selected group?

[Justin Lemkul]

On 11/23/17 11:20 AM, ZHANG Cheng wrote:

Dear Gromacs,
When I calculate the RMSD for the whole protein, I got values mostly from 
0.2-0.5 nm. However, when I only calculate for a particular residue (using an 
index file), the scale is mostly only 0.01-0.02 nm, even for a residue on the 
loop.


My understanding is: when doing the RMSD, the software will align the selected 
group to the group in the reference, as much as possible. Then the software 
calculates the root mean square deviation.


As a result, though a protein may deviate a lot from its reference structure, 
if only one residue is selected for RMSD, the relative positions of the atoms 
within that residue still remain almost the same relative coordination, which 
makes their RMSD only 0.01-0.02 nm.


Can I ask if my understanding is correct?


Yes, but note that fitting a residue to itself is practically useless 
(as you are seeing with your inconsequential residue RMSD values); one 
would more often fit to the whole protein (or backbone, CA, etc) and 
subsequently calculate the RMSD of a given residue if its changes are of 
interest.




I wonder, if I can write some script (e.g. python) to manually extract the 
coordinates information from various frames in the xtc/trr file?


Sure, but you can also do that with gmx traj -ox.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] THE max number of atoms in gromacs?

[Jerry Binder]

Amazing! Thank you so much!

On Fri, Nov 24, 2017 at 5:22 AM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> Hi,
>
> The PDB format is fixed, so it's not really a gromacs problem *per se*.
> Take a look at this
>  content/format33/sect9.html>
> :
>
> "A model cannot have more than 99,999 atoms. Where the entry does not
> contain an ensemble of models, then the entry cannot have more than 99,999
> atoms. Entries that go beyond this atom limit must be split into multiple
> entries, each containing no more than the limits specified above."
>
> You could go around this by writing your model in the gro format instead,
> which allows you to go over 99.999 atoms by simply restarting the atom
> numbering from 0 once you hit 100.000.
>
> J
>
>
>
> On Thu, Nov 23, 2017 at 10:01 PM, Jerry Binder  >
> wrote:
>
> > Hello gmx-users:
> >
> > I build a large system with more than 10,000 atoms, however I cannot
> > write info to pdb file correctly. The pdb file format in gromacs
> > specify 5 positions for atom-id, and it will cause problem if not.
> > Since I have to use rtp file and "pdb2gmx" command to generate
> > conf.gro and topol.top file, a pdb file with >10 atoms is needed.
> >
> > How can I do with it?
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] THE max number of atoms in gromacs?

[João Henriques]

Hi,

The PDB format is fixed, so it's not really a gromacs problem *per se*.
Take a look at this

:

"A model cannot have more than 99,999 atoms. Where the entry does not
contain an ensemble of models, then the entry cannot have more than 99,999
atoms. Entries that go beyond this atom limit must be split into multiple
entries, each containing no more than the limits specified above."

You could go around this by writing your model in the gro format instead,
which allows you to go over 99.999 atoms by simply restarting the atom
numbering from 0 once you hit 100.000.

J



On Thu, Nov 23, 2017 at 10:01 PM, Jerry Binder 
wrote:

> Hello gmx-users:
>
> I build a large system with more than 10,000 atoms, however I cannot
> write info to pdb file correctly. The pdb file format in gromacs
> specify 5 positions for atom-id, and it will cause problem if not.
> Since I have to use rtp file and "pdb2gmx" command to generate
> conf.gro and topol.top file, a pdb file with >10 atoms is needed.
>
> How can I do with it?
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] THE max number of atoms in gromacs?

[Jerry Binder]

Hello gmx-users:

I build a large system with more than 10,000 atoms, however I cannot
write info to pdb file correctly. The pdb file format in gromacs
specify 5 positions for atom-id, and it will cause problem if not.
Since I have to use rtp file and "pdb2gmx" command to generate
conf.gro and topol.top file, a pdb file with >10 atoms is needed.

How can I do with it?
-- 
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Re: [gmx-users] Regarding calculating the water orientation profile

[João Henriques]

Wait, now I remember, you even approached me in a private message and we
exchanged quite a few emails. Did you try any of my suggestions? No success?

J

On Thu, Nov 23, 2017 at 7:36 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> Hi,
>
> I clearly remember replying to something similar sometime ago, and I'm
> almost sure the post was yours. It may be a good idea to rummage through
> the mailing list, because I'm pretty sure this type of analysis has been
> discussed here more than once.
>
> Cheers,
> J
>
> On Thu, Nov 23, 2017 at 4:41 PM, Dilip H N 
> wrote:
>
>> I want to calculate whether the water molecules are coming closer towards
>> the N-terminal or towards the C-terminal of the amino-acid throughout  the
>> simualtion.
>> And hence it can shed some light on the Hydrogen bond
>> dynamicshopefully...
>>
>> Thank you
>>
>>
>>
>>  Sent with Mailtrack
>> > il-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&
>> utm_medium=signature&utm_campaign=signaturevirality>
>>
>> On Thu, Nov 23, 2017 at 6:05 PM, Mark Abraham 
>> wrote:
>>
>> > Hi,
>> >
>> > It sounds like to need to be more clear about what you want to calculate
>> > before you can sensibly find a tool to do it. You should be able to
>> write
>> > down the equation for what you want to compute as your observation long
>> > before you run a simulation, or how will you know what data to collect?
>> >
>> > Mark
>> >
>> > On Thu, 23 Nov 2017 07:26 Dilip H N  wrote:
>> >
>> > > Hello Sir,
>> > > I have run a simulation of amino-acid (glycine) with water molecules
>> for
>> > 10
>> > > ns. Now i need to find out/analyze that whether the water molecules
>> are
>> > > getting/more oriented towards N-terminal of glycine or towards the
>> > > C-terminal of glycine. (i hope this is what water orientation profile
>> > means
>> > > ie., the preferential orientation of water towards particular
>> > > moeity/group...).
>> > > So, which is the exact module/command to find this..?? wether gmx
>> sorient
>> > > or gmx gangle or gmx angle ..??
>> > >
>> > > How to resolve this issue...
>> > >
>> > > Thank you
>> > >
>> > >
>> > > --
>> > > With Best Regards,
>> > >
>> > > DILIP.H.N
>> > > Ph.D Student
>> > >
>> > >
>> > >
>> > > ‌
>> > >  Sent with Mailtrack
>> > > <
>> > > https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/
>> > ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_
>> > medium=signature&utm_campaign=signaturevirality
>> > > >
>> > > --
>> > > 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-requ...@gromacs.org.
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at http://www.gromacs.org/
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>>
>> DILIP.H.N
>> Ph.D Student
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Re: [gmx-users] Regarding calculating the water orientation profile

[João Henriques]

Hi,

I clearly remember replying to something similar sometime ago, and I'm
almost sure the post was yours. It may be a good idea to rummage through
the mailing list, because I'm pretty sure this type of analysis has been
discussed here more than once.

Cheers,
J

On Thu, Nov 23, 2017 at 4:41 PM, Dilip H N 
wrote:

> I want to calculate whether the water molecules are coming closer towards
> the N-terminal or towards the C-terminal of the amino-acid throughout  the
> simualtion.
> And hence it can shed some light on the Hydrogen bond
> dynamicshopefully...
>
> Thank you
>
>
>
>  Sent with Mailtrack
>  ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_
> medium=signature&utm_campaign=signaturevirality>
>
> On Thu, Nov 23, 2017 at 6:05 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > It sounds like to need to be more clear about what you want to calculate
> > before you can sensibly find a tool to do it. You should be able to write
> > down the equation for what you want to compute as your observation long
> > before you run a simulation, or how will you know what data to collect?
> >
> > Mark
> >
> > On Thu, 23 Nov 2017 07:26 Dilip H N  wrote:
> >
> > > Hello Sir,
> > > I have run a simulation of amino-acid (glycine) with water molecules
> for
> > 10
> > > ns. Now i need to find out/analyze that whether the water molecules are
> > > getting/more oriented towards N-terminal of glycine or towards the
> > > C-terminal of glycine. (i hope this is what water orientation profile
> > means
> > > ie., the preferential orientation of water towards particular
> > > moeity/group...).
> > > So, which is the exact module/command to find this..?? wether gmx
> sorient
> > > or gmx gangle or gmx angle ..??
> > >
> > > How to resolve this issue...
> > >
> > > Thank you
> > >
> > >
> > > --
> > > With Best Regards,
> > >
> > > DILIP.H.N
> > > Ph.D Student
> > >
> > >
> > >
> > > ‌
> > >  Sent with Mailtrack
> > > <
> > > https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/
> > ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_
> > medium=signature&utm_campaign=signaturevirality
> > > >
> > > --
> > > 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-requ...@gromacs.org.
> > --
> > 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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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
>
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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[gmx-users] Build thin film.

[ali akgün]

I have a pdb file can i build thin film  ?
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[gmx-users] Does RMSD only consider the "relative" coordinate changes for the selected group?

[ZHANG Cheng]

Dear Gromacs,
When I calculate the RMSD for the whole protein, I got values mostly from 
0.2-0.5 nm. However, when I only calculate for a particular residue (using an 
index file), the scale is mostly only 0.01-0.02 nm, even for a residue on the 
loop.


My understanding is: when doing the RMSD, the software will align the selected 
group to the group in the reference, as much as possible. Then the software 
calculates the root mean square deviation.


As a result, though a protein may deviate a lot from its reference structure, 
if only one residue is selected for RMSD, the relative positions of the atoms 
within that residue still remain almost the same relative coordination, which 
makes their RMSD only 0.01-0.02 nm.


Can I ask if my understanding is correct?


I wonder, if I can write some script (e.g. python) to manually extract the 
coordinates information from various frames in the xtc/trr file?


Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] Regarding calculating the water orientation profile

[Dilip H N]

I want to calculate whether the water molecules are coming closer towards
the N-terminal or towards the C-terminal of the amino-acid throughout  the
simualtion.
And hence it can shed some light on the Hydrogen bond
dynamicshopefully...

Thank you



 Sent with Mailtrack


On Thu, Nov 23, 2017 at 6:05 PM, Mark Abraham 
wrote:

> Hi,
>
> It sounds like to need to be more clear about what you want to calculate
> before you can sensibly find a tool to do it. You should be able to write
> down the equation for what you want to compute as your observation long
> before you run a simulation, or how will you know what data to collect?
>
> Mark
>
> On Thu, 23 Nov 2017 07:26 Dilip H N  wrote:
>
> > Hello Sir,
> > I have run a simulation of amino-acid (glycine) with water molecules for
> 10
> > ns. Now i need to find out/analyze that whether the water molecules are
> > getting/more oriented towards N-terminal of glycine or towards the
> > C-terminal of glycine. (i hope this is what water orientation profile
> means
> > ie., the preferential orientation of water towards particular
> > moeity/group...).
> > So, which is the exact module/command to find this..?? wether gmx sorient
> > or gmx gangle or gmx angle ..??
> >
> > How to resolve this issue...
> >
> > Thank you
> >
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> >
> >
> >
> > ‌
> >  Sent with Mailtrack
> > <
> > https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/
> ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_
> medium=signature&utm_campaign=signaturevirality
> > >
> > --
> > 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-requ...@gromacs.org.
> --
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>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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Re: [gmx-users] Topology file of molecule

[Justin Lemkul]

On 11/23/17 7:51 AM, Magnus Lundborg wrote:

Dear Krzysztof,

I wouldn't be too worried about the fact that GAFF parameters have 
been used for proper and improper torsion angles. It happens quite a 
lot with the OPLS-AA forcefield. But as always, it is good to verify 
that the topology behaves as expected. Unfortunately there is no 
objective way to do this. If there are no experimentally measured 
properties available of your molecule it is a bit risky to proceed. 
However, I would recommend running short simulations of the molecule 
in vacuum (NVT) and in a simulation box solvated by itself just to see 
that it does at least not behave very strangely. If it seems OK I 
think you can proceed with your studies, but as always with an eye 
open for strange behaviour.




The rigorous test is to perform a QM energy scan over the dihedral. 
Rotate in increments of 15 degrees, optimize, and calculate the energy. 
This gives you a one-dimensional potential energy surface. Do the 
corresponding MM evaluations with the force field (in vacuo) and verify 
that the positions and magnitudes of the minima are comparable. If 
they're not, you need to do some refinement of the parameters. Otherwise 
it is extremely hard to define what "strange" is in a simulation; you 
don't know what the molecule should be doing in the first place.


-Justin


I hope that helps you.

Best regards,

Magnus

On 2017-11-23 10:24, Krzysztof Kolman wrote:

Dear Gromacs Users,

I would like to perform a simulation of adsorption of 
3,4-Dihydroxybenzoic

acid (34DHBA) on silica surface using the OPLS-AA forcefield. I created
topology files for the silica surface based on the information found in
papers describing simulations of quartz (Wensink 2000
- 10.1021/la053284f, van der Spoel 2006 -10.1021/la053284f ). The 
topology

for 34DHBA was created using STaGE script (Lundborg 2015
- 10.1021/jp505332p) but some of the parameters (dihedrals) were missing
and GAFF parameters were used instead. Please find below the content 
of itp

file:

[ moleculetype ]
; Name    nrexcl
  34DHBA_opls 3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
  bond_type
   1    opls_145 1   LIG   C1    1 -0.115000   12.01100 ; -0.115000
  CA
   2    opls_166 1   LIG   C2    2  0.15   12.01100 ; 0.035000
  CA
   3    opls_166 1   LIG   C3    3  0.15   12.01100 ; 0.185000
  CA
   4    opls_145 1   LIG   C4    4 -0.115000   12.01100 ; 0.07
  CA
   5    opls_145 1   LIG   C5    5 -0.115000   12.01100 ; -0.045000
  CA
   6    opls_145 1   LIG   C6    6 -0.115000   12.01100 ; -0.16
  CA
   7    opls_167 1   LIG   OC3   7 -0.585000   15.99940 ; -0.745000
  OH
   8    opls_167 1   LIG   OC2   8 -0.585000   15.99940 ; -1.33
  OH
   9    opls_470 1   LIG   C9    9  0.635000   12.01100 ; -0.695000
  C
   10   opls_269 1   LIG   OC91  10    -0.44   15.99940 ; -1.135000
  O_3
   11   opls_268 1   LIG   OC92  11    -0.53   15.99940 ; -1.665000
  OH
   12   opls_146 1   LIG   HC1   12 0.115000    1.00800 ; -1.55
  HA
   13   opls_146 1   LIG   HC4   13 0.115000    1.00800 ; -1.435000
  HA
   14   opls_146 1   LIG   HC6   14 0.115000    1.00800 ; -1.32
  HA
   15   opls_168 1   LIG   HO3   15 0.435000    1.00800 ; -0.885000
  HO
   16   opls_168 1   LIG   HO2   16 0.435000    1.00800 ; -0.45
  HO
   17   opls_270 1   LIG   HO92  17 0.45    1.00800 ; 0.00
  HO

[ bonds ]
;   ai aj funct   r k
 1   2   1   1.4000e-01   3.9246e+05 ; CA - CA
 1   6   1   1.4000e-01   3.9246e+05 ; CA - CA
 1   12   1   1.0800e-01   3.0711e+05 ; CA - HA
 2   3   1   1.4000e-01   3.9246e+05 ; CA - CA
 2   8   1   1.3640e-01   3.7656e+05 ; CA - OH
 3   4   1   1.4000e-01   3.9246e+05 ; CA - CA
 3   7   1   1.3640e-01   3.7656e+05 ; CA - OH
 4   5   1   1.4000e-01   3.9246e+05 ; CA - CA
 4   13   1   1.0800e-01   3.0711e+05 ; CA - HA
 5   6   1   1.4000e-01   3.9246e+05 ; CA - CA
 5   9   1   1.4900e-01   3.3472e+05 ; CA - C
 6   14   1   1.0800e-01   3.0711e+05 ; CA - HA
 7   15   1   9.4500e-02   4.6275e+05 ; OH - HO
 8   16   1   9.4500e-02   4.6275e+05 ; OH - HO
 9   10   1   1.2290e-01   4.7698e+05 ; C - O_3
 9   11   1   1.3640e-01   3.7656e+05 ; C - OH
 11   17   1   9.4500e-02   4.6275e+05 ; OH - HO

[ pairs ]
;   ai aj    funct
  1  4  1 ; C1 - C4
  1  7  1 ; C1 - OC3
  1  9  1 ; C1 - C9
  1 16  1 ; C1 - HO2
  2  5  1 ; C2 - C5
  2 13  1 ; C2 - HC4
  2 14  1 ; C2 - HC6
  2 15  1 ; C2 - HO3
  3  9  1 ; C3 - C9
  3 16  1 ; C3 - HO2
  4  8  1 ; C4 - OC2
  4 10  1 ; C4 - OC91
  4 11  1 ; C4 - OC92
  4 14  1 ; C4 - HC6
  4 15  1 ; C4 - 

Re: [gmx-users] Topology file of molecule

[Magnus Lundborg]

Dear Krzysztof,

I wouldn't be too worried about the fact that GAFF parameters have been 
used for proper and improper torsion angles. It happens quite a lot with 
the OPLS-AA forcefield. But as always, it is good to verify that the 
topology behaves as expected. Unfortunately there is no objective way to 
do this. If there are no experimentally measured properties available of 
your molecule it is a bit risky to proceed. However, I would recommend 
running short simulations of the molecule in vacuum (NVT) and in a 
simulation box solvated by itself just to see that it does at least not 
behave very strangely. If it seems OK I think you can proceed with your 
studies, but as always with an eye open for strange behaviour.


I hope that helps you.

Best regards,

Magnus

On 2017-11-23 10:24, Krzysztof Kolman wrote:

Dear Gromacs Users,

I would like to perform a simulation of adsorption of 3,4-Dihydroxybenzoic
acid (34DHBA) on silica surface using the OPLS-AA forcefield. I created
topology files for the silica surface based on the information found in
papers describing simulations of quartz (Wensink 2000
- 10.1021/la053284f, van der Spoel 2006 -10.1021/la053284f ). The topology
for 34DHBA was created using STaGE script (Lundborg 2015
- 10.1021/jp505332p) but some of the parameters (dihedrals) were missing
and GAFF parameters were used instead. Please find below the content of itp
file:

[ moleculetype ]
; Namenrexcl
  34DHBA_opls 3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
  bond_type
   1opls_145 1   LIG   C11 -0.115000   12.01100 ; -0.115000
  CA
   2opls_166 1   LIG   C22  0.15   12.01100 ; 0.035000
  CA
   3opls_166 1   LIG   C33  0.15   12.01100 ; 0.185000
  CA
   4opls_145 1   LIG   C44 -0.115000   12.01100 ; 0.07
  CA
   5opls_145 1   LIG   C55 -0.115000   12.01100 ; -0.045000
  CA
   6opls_145 1   LIG   C66 -0.115000   12.01100 ; -0.16
  CA
   7opls_167 1   LIG   OC3   7 -0.585000   15.99940 ; -0.745000
  OH
   8opls_167 1   LIG   OC2   8 -0.585000   15.99940 ; -1.33
  OH
   9opls_470 1   LIG   C99  0.635000   12.01100 ; -0.695000
  C
   10   opls_269 1   LIG   OC91  10-0.44   15.99940 ; -1.135000
  O_3
   11   opls_268 1   LIG   OC92  11-0.53   15.99940 ; -1.665000
  OH
   12   opls_146 1   LIG   HC1   12 0.1150001.00800 ; -1.55
  HA
   13   opls_146 1   LIG   HC4   13 0.1150001.00800 ; -1.435000
  HA
   14   opls_146 1   LIG   HC6   14 0.1150001.00800 ; -1.32
  HA
   15   opls_168 1   LIG   HO3   15 0.4350001.00800 ; -0.885000
  HO
   16   opls_168 1   LIG   HO2   16 0.4350001.00800 ; -0.45
  HO
   17   opls_270 1   LIG   HO92  17 0.451.00800 ; 0.00
  HO

[ bonds ]
;   ai aj funct   r k
 1   2   1   1.4000e-01   3.9246e+05 ; CA - CA
 1   6   1   1.4000e-01   3.9246e+05 ; CA - CA
 1   12   1   1.0800e-01   3.0711e+05 ; CA - HA
 2   3   1   1.4000e-01   3.9246e+05 ; CA - CA
 2   8   1   1.3640e-01   3.7656e+05 ; CA - OH
 3   4   1   1.4000e-01   3.9246e+05 ; CA - CA
 3   7   1   1.3640e-01   3.7656e+05 ; CA - OH
 4   5   1   1.4000e-01   3.9246e+05 ; CA - CA
 4   13   1   1.0800e-01   3.0711e+05 ; CA - HA
 5   6   1   1.4000e-01   3.9246e+05 ; CA - CA
 5   9   1   1.4900e-01   3.3472e+05 ; CA - C
 6   14   1   1.0800e-01   3.0711e+05 ; CA - HA
 7   15   1   9.4500e-02   4.6275e+05 ; OH - HO
 8   16   1   9.4500e-02   4.6275e+05 ; OH - HO
 9   10   1   1.2290e-01   4.7698e+05 ; C - O_3
 9   11   1   1.3640e-01   3.7656e+05 ; C - OH
 11   17   1   9.4500e-02   4.6275e+05 ; OH - HO

[ pairs ]
;   ai ajfunct
  1  4  1 ; C1 - C4
  1  7  1 ; C1 - OC3
  1  9  1 ; C1 - C9
  1 16  1 ; C1 - HO2
  2  5  1 ; C2 - C5
  2 13  1 ; C2 - HC4
  2 14  1 ; C2 - HC6
  2 15  1 ; C2 - HO3
  3  9  1 ; C3 - C9
  3 16  1 ; C3 - HO2
  4  8  1 ; C4 - OC2
  4 10  1 ; C4 - OC91
  4 11  1 ; C4 - OC92
  4 14  1 ; C4 - HC6
  4 15  1 ; C4 - HO3
  5  7  1 ; C5 - OC3
  5 17  1 ; C5 - HO92
  6  3  1 ; C6 - C3
  6  8  1 ; C6 - OC2
  6 10  1 ; C6 - OC91
  6 11  1 ; C6 - OC92
  6 13  1 ; C6 - HC4
  7  8  1 ;OC3 - OC2
  7 13  1 ;OC3 - HC4
  9 13  1 ; C9 - HC4
  9 14  1 ; C9 - HC6
 10 17  1 ;   OC91 - HO92
 12  3  1 ;HC1 - C3
 12  5  1 ;HC1 - C5
 12  8  1 ;HC1 - OC2

Re: [gmx-users] Restarting simulation from not last checkpoint but previous to last check point

[Mark Abraham]

Hi,

Yes. Back up your files, then start using -cpi state_prev.cpt as part of
your mdrun command.

Mark

On Thu, 23 Nov 2017 12:13 atb files  wrote:

>
>
>
>
> Hi Experts,I am restarting the simulation using command gmx
> mdrun -deffnm name -v -c -s topol.tpr -cpi name.cpt -appendGromacs giving
> error that your checkpoint file is empty/currupted, it happened due to disk
> space. Can I set checkpoint not latest but the one before the latest
> checkpoint.Any help?YogiSent using Zoho Mail
>
>
>
>
>
>
>
>
> --
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> posting!
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Regarding calculating the water orientation profile

[Mark Abraham]

Hi,

It sounds like to need to be more clear about what you want to calculate
before you can sensibly find a tool to do it. You should be able to write
down the equation for what you want to compute as your observation long
before you run a simulation, or how will you know what data to collect?

Mark

On Thu, 23 Nov 2017 07:26 Dilip H N  wrote:

> Hello Sir,
> I have run a simulation of amino-acid (glycine) with water molecules for 10
> ns. Now i need to find out/analyze that whether the water molecules are
> getting/more oriented towards N-terminal of glycine or towards the
> C-terminal of glycine. (i hope this is what water orientation profile means
> ie., the preferential orientation of water towards particular
> moeity/group...).
> So, which is the exact module/command to find this..?? wether gmx sorient
> or gmx gangle or gmx angle ..??
>
> How to resolve this issue...
>
> Thank you
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
> ‌
>  Sent with Mailtrack
> <
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Re: [gmx-users] how to set hetrodimer for MD Simulation

[Erik Marklund]

Dear Rana,

a) We are not (necessarily) Amber users. This is a gromacs mailing list.

b) If the separate structures are correctly positioned relative to each other, 
you basically just need to cut-and-paste the ATOM records from one pdb file 
into the other one.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 22 Nov 2017, at 22:15, Rana Rehan Khalid 
mailto:rrkha...@umich.edu>> wrote:

Dear Amber users

My protein system consist of two subunit chains alpha and beta each chain
consist four domains. I predicted the structure of both subunit chains now
i want to combine both structure  subunits models, How i can combine them
in one pdb file.  so that i can run the simulation on complete structure.
Kindly guide me.

Regards
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[gmx-users] Restarting simulation from not last checkpoint but previous to last check point

[atb files]

Hi Experts,I am restarting the simulation using command gmx mdrun 
-deffnm name -v -c -s topol.tpr -cpi name.cpt -appendGromacs giving error that 
your checkpoint file is empty/currupted, it happened due to disk space. Can I 
set checkpoint not latest but the one before the latest checkpoint.Any 
help?YogiSent using Zoho Mail








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[gmx-users] Topology file of molecule

[Krzysztof Kolman]

Dear Gromacs Users,

I would like to perform a simulation of adsorption of 3,4-Dihydroxybenzoic
acid (34DHBA) on silica surface using the OPLS-AA forcefield. I created
topology files for the silica surface based on the information found in
papers describing simulations of quartz (Wensink 2000
- 10.1021/la053284f, van der Spoel 2006 -10.1021/la053284f ). The topology
for 34DHBA was created using STaGE script (Lundborg 2015
- 10.1021/jp505332p) but some of the parameters (dihedrals) were missing
and GAFF parameters were used instead. Please find below the content of itp
file:

[ moleculetype ]
; Namenrexcl
 34DHBA_opls 3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
 bond_type
  1opls_145 1   LIG   C11 -0.115000   12.01100 ; -0.115000
 CA
  2opls_166 1   LIG   C22  0.15   12.01100 ; 0.035000
 CA
  3opls_166 1   LIG   C33  0.15   12.01100 ; 0.185000
 CA
  4opls_145 1   LIG   C44 -0.115000   12.01100 ; 0.07
 CA
  5opls_145 1   LIG   C55 -0.115000   12.01100 ; -0.045000
 CA
  6opls_145 1   LIG   C66 -0.115000   12.01100 ; -0.16
 CA
  7opls_167 1   LIG   OC3   7 -0.585000   15.99940 ; -0.745000
 OH
  8opls_167 1   LIG   OC2   8 -0.585000   15.99940 ; -1.33
 OH
  9opls_470 1   LIG   C99  0.635000   12.01100 ; -0.695000
 C
  10   opls_269 1   LIG   OC91  10-0.44   15.99940 ; -1.135000
 O_3
  11   opls_268 1   LIG   OC92  11-0.53   15.99940 ; -1.665000
 OH
  12   opls_146 1   LIG   HC1   12 0.1150001.00800 ; -1.55
 HA
  13   opls_146 1   LIG   HC4   13 0.1150001.00800 ; -1.435000
 HA
  14   opls_146 1   LIG   HC6   14 0.1150001.00800 ; -1.32
 HA
  15   opls_168 1   LIG   HO3   15 0.4350001.00800 ; -0.885000
 HO
  16   opls_168 1   LIG   HO2   16 0.4350001.00800 ; -0.45
 HO
  17   opls_270 1   LIG   HO92  17 0.451.00800 ; 0.00
 HO

[ bonds ]
;   ai aj funct   r k
1   2   1   1.4000e-01   3.9246e+05 ; CA - CA
1   6   1   1.4000e-01   3.9246e+05 ; CA - CA
1   12   1   1.0800e-01   3.0711e+05 ; CA - HA
2   3   1   1.4000e-01   3.9246e+05 ; CA - CA
2   8   1   1.3640e-01   3.7656e+05 ; CA - OH
3   4   1   1.4000e-01   3.9246e+05 ; CA - CA
3   7   1   1.3640e-01   3.7656e+05 ; CA - OH
4   5   1   1.4000e-01   3.9246e+05 ; CA - CA
4   13   1   1.0800e-01   3.0711e+05 ; CA - HA
5   6   1   1.4000e-01   3.9246e+05 ; CA - CA
5   9   1   1.4900e-01   3.3472e+05 ; CA - C
6   14   1   1.0800e-01   3.0711e+05 ; CA - HA
7   15   1   9.4500e-02   4.6275e+05 ; OH - HO
8   16   1   9.4500e-02   4.6275e+05 ; OH - HO
9   10   1   1.2290e-01   4.7698e+05 ; C - O_3
9   11   1   1.3640e-01   3.7656e+05 ; C - OH
11   17   1   9.4500e-02   4.6275e+05 ; OH - HO

[ pairs ]
;   ai ajfunct
 1  4  1 ; C1 - C4
 1  7  1 ; C1 - OC3
 1  9  1 ; C1 - C9
 1 16  1 ; C1 - HO2
 2  5  1 ; C2 - C5
 2 13  1 ; C2 - HC4
 2 14  1 ; C2 - HC6
 2 15  1 ; C2 - HO3
 3  9  1 ; C3 - C9
 3 16  1 ; C3 - HO2
 4  8  1 ; C4 - OC2
 4 10  1 ; C4 - OC91
 4 11  1 ; C4 - OC92
 4 14  1 ; C4 - HC6
 4 15  1 ; C4 - HO3
 5  7  1 ; C5 - OC3
 5 17  1 ; C5 - HO92
 6  3  1 ; C6 - C3
 6  8  1 ; C6 - OC2
 6 10  1 ; C6 - OC91
 6 11  1 ; C6 - OC92
 6 13  1 ; C6 - HC4
 7  8  1 ;OC3 - OC2
 7 13  1 ;OC3 - HC4
 9 13  1 ; C9 - HC4
 9 14  1 ; C9 - HC6
10 17  1 ;   OC91 - HO92
12  3  1 ;HC1 - C3
12  5  1 ;HC1 - C5
12  8  1 ;HC1 - OC2
12 14  1 ;HC1 - HC6

[ angles ]
;   ai aj akfunct   theta cth
1   2   3   1   1.2000e+02   5.2718e+02 ; CA - CA - CA
1   2   8   1   1.2000e+02   5.8576e+02 ; CA - CA - OH
1   6   5   1   1.2000e+02   5.2718e+02 ; CA - CA - CA
1   6   14   1   1.2000e+02   2.9288e+02 ; CA - CA - HA
2   1   6   1   1.2000e+02   5.2718e+02 ; CA - CA - CA
2   1   12   1   1.2000e+02   2.9288e+02 ; CA - CA - HA
2   3   4   1   1.2000e+02   5.2718e+02 ; CA - CA - CA
2   3   7   1   1.2000e+02   5.8576e+02 ; CA - CA - OH
2   8   16   1   1.1300e+02   2.9288e+02 ; CA - OH - HO
3   2   8   1   1.2000e+02   5.8576e+02 ; CA - CA - OH
3   4   5   1   1.2000e+02   5.2718e+02 ; CA - CA - CA
3   4   13   1   1.2000e+02   2.9288e+02 ; CA - CA - HA
3   7   15   1   1.1300e+02   2.9288e+02 ; CA - OH - HO
4   3   7   1   1.2000e+02   5.8576e