Re: [gmx-users] Error No default Proper Dih. types

2020-04-26 Thread Paolo Costa 
Dear Justin,

thanks a lot.

Paolo

Il giorno dom 26 apr 2020 alle ore 22:33 Justin Lemkul  ha
scritto:

>
>
> On 4/26/20 3:53 PM, Paolo Costa wrote:
> > Dear Justin,
> >
> > thanks for your extra description. Very nice!
> > Last doubt, which values of "phase" and "pn" should I use for [
> > dihedraltypes ]?
>
> If the force constant is zero, the remaining parameters are irrelevant.
>
> -Justin
>
> > Thanks again.
> >
> > Paolo
> >
> > Il giorno dom 26 apr 2020 alle ore 20:33 Justin Lemkul 
> ha
> > scritto:
> >
> >>
> >> On 4/26/20 2:08 PM, Paolo Costa wrote:
> >>> Dear Justin,
> >>>
> >>> thanks a  lot for your quick reply and useful information.
> >>> Thus, I will go through to all the dihedral terms and define zero the
> >>> corresponding force constant as you suggested. In any case, I guess it
> >> will
> >>> be too much work to calculate also the force constant for the torsion
> >> angle
> >>> rotation.
> >> Metals are usually the bridge point between multiple groups and as such
> >> their dihedrals are all coupled and not generally considered "soft"
> >> (rotatable). So the conformational energetics of these molecules usually
> >> involves only bonds and angles in terms of internal parameters.
> >>
> >> -Justin
> >>
> >>> Thanks again.
> >>>
> >>> Paolo
> >>>
> >>> Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul <
> jalem...@vt.edu>
> >> ha
> >>> scritto:
> >>>
>  On 4/26/20 1:57 PM, Paolo Costa wrote:
> > Dear Gromacs users,
> >
> > within Amber99 force field I created a new molecule,
> polyoxometallate,
> >> by
> > creating a new .rtp file and modifying the atomtypes.atp,
> >> ffnonbonded.itp
> > and the ffbondend.itp. For the ffnonbonded.itp I took the LJ
> parameters
> > from known works, while the parameters for the bonding interactions I
> > determined by Gaussian together with VFFDT software.
> > I did not insert any parameters for the dihedral angles since the
> >> VFFTDT
> > software does not calculated them. However as written in the related
>  paper
> > (J. Chem. Inf. Model. 2016, 56, 811−818), *"Torsion angle rotation
>  related
> > to metals can often be ignored".*
> > Does somebody knows how to overcome such error in Gromacs?
>  pdb2gmx generates all possible angles and dihedrals, as determined by
>  the bonds that are defined in the .rtp entry. Thus, you likely have
>  dihedrals in the topology in which one of the participating atoms is
> the
>  metal. You have to have parameters for all defined interactions, but
> it
>  is true that dihedral terms are not typically used in this case. The
>  simplest solution is to define dihedrals with zero force constants so
>  they do not contribute to the forces in the system.
> 
>  -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
> 
>  jalem...@vt.edu | (540) 231-3129
>  http://www.thelemkullab.com
> 
>  ==
> 
>  --
>  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.
> >>>
> >> --
> >> ==
> >>
> >> 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
> >>
> >> jalem...@vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==
> >>
> >> --
> >> 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.
> >
> >
>
> --
> ==
>
> 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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
>

[gmx-users] about how to create covar.ndx for dihedral Principal Component Analysis

2020-04-26 Thread lazaro monteserin 
Dear Gromacs users,

I am trying to run a dPCA to select the best conformation from my
trajectory.

When I follow the steps in gromacs manual I have a question about one of
the steps:

3. Make an index file
, named as
covar.ndx, which necessarily contains one group of atom 1 to
integer(2*N/3), where N is the number of dihedral angles. For example, for
a peptide of 5 dihedral angles

How can I create the covar.ndx? How could I use gmx make_ndx for this?

In my case I have 99 atoms and 66 cos/sin integrals. So I guess the
covar.ndx should has one group with atoms numbers from 1 2 3 4 5... to 66?

Should I have to do this in a text editor by hand?

Kindly,

Lazaro
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[gmx-users] Atom CA used in that entry is not found in the input file

2020-04-26 Thread Daniel Burns 
Hello,

I edited a few selenomethionine residues, changing "S" to "SD" and removed
the "SE" at the end of the line.  I then ran pdb2gmx with Charmm36.  I get
the following error (not sure why the residue number doesn't match):

Fatal error:
Residue 324 named GLY of a molecule in the input file was mapped
to an entry in the topology database, but the atom CA used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

My .pdb file section looks like this:
ATOM569  N   MET A 324  87.364  46.446  53.851  1.00  3.42
  N
ATOM570  CA  MET A 324  86.617  45.972  52.679  1.00  6.50
  C
ATOM571  C   MET A 324  87.405  46.212  51.424  1.00  6.43
  C
ATOM572  O   MET A 324  86.987  45.830  50.332  1.00  8.80
  O
ATOM573  CB  MET A 324  85.203  46.573  52.584  1.00  5.66
  C
ATOM574  CG  MET A 324  84.258  46.053  53.663  1.00  5.50
  C
ATOM575  CE  MET A 324  83.200  44.225  51.772  1.00  3.19
  C
ATOM576  SD  MET A 324  83.876  44.132  53.563  1.00 14.27
  S
ATOM577  N   GLY A 325  88.553  46.854  51.604  1.00  9.51
  N
ATOM578  CA  GLY A 325  89.548  47.012  50.546  1.00  9.78
  C
ATOM579  C   GLY A 325  89.087  47.608  49.227  1.00  9.91
  C
ATOM580  O   GLY A 325  89.352  47.048  48.159  1.00 11.43
  O
ATOM581  N   GLY A 326  88.403  48.742  49.271  1.00  7.35
  N
ATOM582  CA  GLY A 326  87.942  49.290  48.005  1.00  6.34
  C
ATOM583  C   GLY A 326  86.542  48.875  47.602  1.00  3.91
  C
ATOM584  O   GLY A 326  85.947  49.547  46.765  1.00  4.00
  O

I don't see anything wrong with my GLY residues and none of the other
Glycines are presenting an error.  This does follow one of my edited MET
residues.

Thank you,

Dan
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Re: [gmx-users] Error No default Proper Dih. types

2020-04-26 Thread Justin Lemkul 



On 4/26/20 3:53 PM, Paolo Costa wrote:

Dear Justin,

thanks for your extra description. Very nice!
Last doubt, which values of "phase" and "pn" should I use for [
dihedraltypes ]?


If the force constant is zero, the remaining parameters are irrelevant.

-Justin


Thanks again.

Paolo

Il giorno dom 26 apr 2020 alle ore 20:33 Justin Lemkul  ha
scritto:



On 4/26/20 2:08 PM, Paolo Costa wrote:

Dear Justin,

thanks a  lot for your quick reply and useful information.
Thus, I will go through to all the dihedral terms and define zero the
corresponding force constant as you suggested. In any case, I guess it

will

be too much work to calculate also the force constant for the torsion

angle

rotation.

Metals are usually the bridge point between multiple groups and as such
their dihedrals are all coupled and not generally considered "soft"
(rotatable). So the conformational energetics of these molecules usually
involves only bonds and angles in terms of internal parameters.

-Justin


Thanks again.

Paolo

Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul 

ha

scritto:


On 4/26/20 1:57 PM, Paolo Costa wrote:

Dear Gromacs users,

within Amber99 force field I created a new molecule, polyoxometallate,

by

creating a new .rtp file and modifying the atomtypes.atp,

ffnonbonded.itp

and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters
from known works, while the parameters for the bonding interactions I
determined by Gaussian together with VFFDT software.
I did not insert any parameters for the dihedral angles since the

VFFTDT

software does not calculated them. However as written in the related

paper

(J. Chem. Inf. Model. 2016, 56, 811−818), *"Torsion angle rotation

related

to metals can often be ignored".*
Does somebody knows how to overcome such error in Gromacs?

pdb2gmx generates all possible angles and dihedrals, as determined by
the bonds that are defined in the .rtp entry. Thus, you likely have
dihedrals in the topology in which one of the participating atoms is the
metal. You have to have parameters for all defined interactions, but it
is true that dihedral terms are not typically used in this case. The
simplest solution is to define dihedrals with zero force constants so
they do not contribute to the forces in the system.

-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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--
==

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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--
==

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Error No default Proper Dih. types

2020-04-26 Thread Paolo Costa 
Dear Justin,

thanks for your extra description. Very nice!
Last doubt, which values of "phase" and "pn" should I use for [
dihedraltypes ]?

Thanks again.

Paolo

Il giorno dom 26 apr 2020 alle ore 20:33 Justin Lemkul  ha
scritto:

>
>
> On 4/26/20 2:08 PM, Paolo Costa wrote:
> > Dear Justin,
> >
> > thanks a  lot for your quick reply and useful information.
> > Thus, I will go through to all the dihedral terms and define zero the
> > corresponding force constant as you suggested. In any case, I guess it
> will
> > be too much work to calculate also the force constant for the torsion
> angle
> > rotation.
>
> Metals are usually the bridge point between multiple groups and as such
> their dihedrals are all coupled and not generally considered "soft"
> (rotatable). So the conformational energetics of these molecules usually
> involves only bonds and angles in terms of internal parameters.
>
> -Justin
>
> > Thanks again.
> >
> > Paolo
> >
> > Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul 
> ha
> > scritto:
> >
> >>
> >> On 4/26/20 1:57 PM, Paolo Costa wrote:
> >>> Dear Gromacs users,
> >>>
> >>> within Amber99 force field I created a new molecule, polyoxometallate,
> by
> >>> creating a new .rtp file and modifying the atomtypes.atp,
> ffnonbonded.itp
> >>> and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters
> >>> from known works, while the parameters for the bonding interactions I
> >>> determined by Gaussian together with VFFDT software.
> >>> I did not insert any parameters for the dihedral angles since the
> VFFTDT
> >>> software does not calculated them. However as written in the related
> >> paper
> >>> (J. Chem. Inf. Model. 2016, 56, 811−818), *"Torsion angle rotation
> >> related
> >>> to metals can often be ignored".*
> >>> Does somebody knows how to overcome such error in Gromacs?
> >> pdb2gmx generates all possible angles and dihedrals, as determined by
> >> the bonds that are defined in the .rtp entry. Thus, you likely have
> >> dihedrals in the topology in which one of the participating atoms is the
> >> metal. You have to have parameters for all defined interactions, but it
> >> is true that dihedral terms are not typically used in this case. The
> >> simplest solution is to define dihedrals with zero force constants so
> >> they do not contribute to the forces in the system.
> >>
> >> -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
> >>
> >> jalem...@vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==
> >>
> >> --
> >> 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.
> >
> >
>
> --
> ==
>
> 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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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.



-- 
Paolo Costa, Ph.D.
Postdoctoral Researcher
Department of Chemistry and Biomolecular Sciences
University of Ottawa
10 Marie Curie, Ottawa, ON K1N 6N5, Canada
Room number: DRO 326 (D'Iorio Hall)
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Re: [gmx-users] Error No default Proper Dih. types

2020-04-26 Thread Justin Lemkul 



On 4/26/20 2:08 PM, Paolo Costa wrote:

Dear Justin,

thanks a  lot for your quick reply and useful information.
Thus, I will go through to all the dihedral terms and define zero the
corresponding force constant as you suggested. In any case, I guess it will
be too much work to calculate also the force constant for the torsion angle
rotation.


Metals are usually the bridge point between multiple groups and as such 
their dihedrals are all coupled and not generally considered "soft" 
(rotatable). So the conformational energetics of these molecules usually 
involves only bonds and angles in terms of internal parameters.


-Justin


Thanks again.

Paolo

Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul  ha
scritto:



On 4/26/20 1:57 PM, Paolo Costa wrote:

Dear Gromacs users,

within Amber99 force field I created a new molecule, polyoxometallate, by
creating a new .rtp file and modifying the atomtypes.atp, ffnonbonded.itp
and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters
from known works, while the parameters for the bonding interactions I
determined by Gaussian together with VFFDT software.
I did not insert any parameters for the dihedral angles since the VFFTDT
software does not calculated them. However as written in the related

paper

(J. Chem. Inf. Model. 2016, 56, 811−818), *"Torsion angle rotation

related

to metals can often be ignored".*
Does somebody knows how to overcome such error in Gromacs?

pdb2gmx generates all possible angles and dihedrals, as determined by
the bonds that are defined in the .rtp entry. Thus, you likely have
dihedrals in the topology in which one of the participating atoms is the
metal. You have to have parameters for all defined interactions, but it
is true that dihedral terms are not typically used in this case. The
simplest solution is to define dihedrals with zero force constants so
they do not contribute to the forces in the system.

-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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--
==

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] wham - Bootstraping

2020-04-26 Thread Alex 
Dear all,
Each windows of a wham analysis is a 30 ns long simulation. And I choose 25
ns of them in gmx wham -b 5000 -nBootstrap 250 -bins 250 -bs-method b-hist
... .

I noticed the below massages in the log file that only 395 , 1854,  and
around 2000 are being evaluated out of 24250 contributions.

Updated rapid wham stuff. (evaluating only 395 of 24250 contributions)
Updated rapid wham stuff. (evaluating only 1854 of 24250 contributions)

Would you please let me know how 395, 1854 ... are being considered for
evaluation? and what do they mean?

Regards,
Alex
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Re: [gmx-users] Error No default Proper Dih. types

2020-04-26 Thread Paolo Costa 
Dear Justin,

thanks a  lot for your quick reply and useful information.
Thus, I will go through to all the dihedral terms and define zero the
corresponding force constant as you suggested. In any case, I guess it will
be too much work to calculate also the force constant for the torsion angle
rotation.

Thanks again.

Paolo

Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul  ha
scritto:

>
>
> On 4/26/20 1:57 PM, Paolo Costa wrote:
> > Dear Gromacs users,
> >
> > within Amber99 force field I created a new molecule, polyoxometallate, by
> > creating a new .rtp file and modifying the atomtypes.atp, ffnonbonded.itp
> > and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters
> > from known works, while the parameters for the bonding interactions I
> > determined by Gaussian together with VFFDT software.
> > I did not insert any parameters for the dihedral angles since the VFFTDT
> > software does not calculated them. However as written in the related
> paper
> > (J. Chem. Inf. Model. 2016, 56, 811−818), *"Torsion angle rotation
> related
> > to metals can often be ignored".*
> > Does somebody knows how to overcome such error in Gromacs?
>
> pdb2gmx generates all possible angles and dihedrals, as determined by
> the bonds that are defined in the .rtp entry. Thus, you likely have
> dihedrals in the topology in which one of the participating atoms is the
> metal. You have to have parameters for all defined interactions, but it
> is true that dihedral terms are not typically used in this case. The
> simplest solution is to define dihedrals with zero force constants so
> they do not contribute to the forces in the system.
>
> -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
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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.



-- 
Paolo Costa, Ph.D.
Postdoctoral Researcher
Department of Chemistry and Biomolecular Sciences
University of Ottawa
10 Marie Curie, Ottawa, ON K1N 6N5, Canada
Room number: DRO 326 (D'Iorio Hall)
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Re: [gmx-users] Error No default Proper Dih. types

2020-04-26 Thread Justin Lemkul 



On 4/26/20 1:57 PM, Paolo Costa wrote:

Dear Gromacs users,

within Amber99 force field I created a new molecule, polyoxometallate, by
creating a new .rtp file and modifying the atomtypes.atp, ffnonbonded.itp
and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters
from known works, while the parameters for the bonding interactions I
determined by Gaussian together with VFFDT software.
I did not insert any parameters for the dihedral angles since the VFFTDT
software does not calculated them. However as written in the related paper
(J. Chem. Inf. Model. 2016, 56, 811−818), *"Torsion angle rotation related
to metals can often be ignored".*
Does somebody knows how to overcome such error in Gromacs?


pdb2gmx generates all possible angles and dihedrals, as determined by 
the bonds that are defined in the .rtp entry. Thus, you likely have 
dihedrals in the topology in which one of the participating atoms is the 
metal. You have to have parameters for all defined interactions, but it 
is true that dihedral terms are not typically used in this case. The 
simplest solution is to define dihedrals with zero force constants so 
they do not contribute to the forces in the system.


-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] Error No default Proper Dih. types

2020-04-26 Thread Paolo Costa 
Dear Gromacs users,

within Amber99 force field I created a new molecule, polyoxometallate, by
creating a new .rtp file and modifying the atomtypes.atp, ffnonbonded.itp
and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters
from known works, while the parameters for the bonding interactions I
determined by Gaussian together with VFFDT software.
I did not insert any parameters for the dihedral angles since the VFFTDT
software does not calculated them. However as written in the related paper
(J. Chem. Inf. Model. 2016, 56, 811−818), *"Torsion angle rotation related
to metals can often be ignored".*
Does somebody knows how to overcome such error in Gromacs?

Thanks a lot.

Paolo

-- 
Paolo Costa, Ph.D.
Postdoctoral Researcher
Department of Chemistry and Biomolecular Sciences
University of Ottawa
10 Marie Curie, Ottawa, ON K1N 6N5, Canada
Room number: DRO 326 (D'Iorio Hall)
-- 
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Re: [gmx-users] gromacs installation (2020&2019)

2020-04-26 Thread lazaro monteserin 
Hey Netaly, are you trying to install Gromacs 2019 and 2020 at the same
time? If not a couple of things to keep in mind.  Be sure before installing
Gromacs you have all the utilities that Gromacs use, compilers, etc and
that their versions are supported. I saw you are trying to install it for
GPU, for that you need to install first the cuda toolkit versión for your
linux. Now if you are installing Gromacs in an Ubuntu virtual machine on
windows this is going to be a big problem. So for this case my
recommendation is install it without GPU. Follow the instructions for
installation in the website. Should work perfectly. Kindly, Lazaro

On Sun, Apr 26, 2020 at 12:07 PM Yu Du  wrote:

> Hi Netaly,
>
> Although I do not know the exact reason of the failure, after skimming
> through your command, I think that you probably need to assign absolute
> path to CMAKE_INSTALL_PREFIX and have access to the internet for
> downloading REGRESSIONTEST and FFTW package.
>
> If you are new to GROMACS, I recommend installation from simple case, such
> as only CPU no GPU. Only after successfully installing CPU only version
> GROMACS, run to the next level CPU+GPU. This step-by-step installation
> practice can give you a feeling of choosing CMake options.
>
> Cheers,
>
> Du, Yu
> PhD Student,
> Shanghai Institute of Organic Chemistry
> 345 Ling Ling Rd., Shanghai, China.
> Zip: 200032, Tel: (86) 021 5492 5275
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Netaly
> Khazanov 
> Sent: Sunday, April 26, 2020 15:38
> To: Discussion list for GROMACS users 
> Subject: [gmx-users] gromacs installation (2020&2019)
>
> Dear All,
> I am trying to install gromacs 2020 and 2019 versions on CentOS release
> 6.10 (Final) linux system.
> I passed throuht cmake compilation. Using command
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on
> -DCMAKE_INSTALL_PREFIX=gromacs2020
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.0 -DGMX_FFT_LIBRARY=fftw3
> -DCMAKE_C_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/cc
> -DCMAKE_CXX_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++
> -DCUDA_HOST_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++
> I've used gcc 5 version (tried also 6 version)
>
> However, I am struggling through make execution :
> in gromacs 2019 -
>
> [ 37%] Built target libgromacs_generated
> [ 37%] Built target libgromacs_external
> Scanning dependencies of target gpu_utilstest_cuda
> [ 37%] Linking CXX shared library ../../../../lib/libgpu_utilstest_cuda.so
> [ 37%] Built target gpu_utilstest_cuda
>
> in gromacs 2020-
> [ 27%] Built target linearalgebra
> [ 27%] Built target scanner
> [ 27%] Built target tng_io_obj
> [ 27%] Built target modularsimulator
>
> It just stuck on the line and doesn't continue to run.
>
> Any suggestions will be appreciated.
> Thanks in advance.
>
>
> --
> Netaly
> --
> 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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>
> * Please search the archive at
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>
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Re: [gmx-users] lincs warning

2020-04-26 Thread Yu Du 
Hi Afsane,

You need to provide more details of the simulation, such as how you generated 
the configuration and topology, what force field you used and so on, or we can 
not give you any advice.

Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China.
Zip: 200032, Tel: (86) 021 5492 5275

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Afsane Farhadi 

Sent: Sunday, April 26, 2020 01:16
To: Discussion List for GROMACS Users 
Subject: [gmx-users] lincs warning

Hi gromacs users I generated a mixed box of methane and carbondioxide with 
insert-molecules (500 methane+62carbondioxide) . The pdb file of methane and 
carbondioxide are optimized and the energy minimization of mixed gas  is ok 
(potential energy is about -2e+03))but when I want to run a npt run ,the lincs 
warning are showing( bond rotate more than 30 degree).I repeated energy 
minimization but it didn't work right Can any body help me please?

Sent from Yahoo Mail on Android
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Re: [gmx-users] gromacs installation (2020&2019)

2020-04-26 Thread Yu Du 
Hi Netaly,

Although I do not know the exact reason of the failure, after skimming through 
your command, I think that you probably need to assign absolute path to 
CMAKE_INSTALL_PREFIX and have access to the internet for downloading 
REGRESSIONTEST and FFTW package.

If you are new to GROMACS, I recommend installation from simple case, such as 
only CPU no GPU. Only after successfully installing CPU only version GROMACS, 
run to the next level CPU+GPU. This step-by-step installation practice can give 
you a feeling of choosing CMake options.

Cheers,

Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China.
Zip: 200032, Tel: (86) 021 5492 5275

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Netaly 
Khazanov 
Sent: Sunday, April 26, 2020 15:38
To: Discussion list for GROMACS users 
Subject: [gmx-users] gromacs installation (2020&2019)

Dear All,
I am trying to install gromacs 2020 and 2019 versions on CentOS release
6.10 (Final) linux system.
I passed throuht cmake compilation. Using command
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on
-DCMAKE_INSTALL_PREFIX=gromacs2020
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.0 -DGMX_FFT_LIBRARY=fftw3
-DCMAKE_C_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/cc
-DCMAKE_CXX_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++
-DCUDA_HOST_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++
I've used gcc 5 version (tried also 6 version)

However, I am struggling through make execution :
in gromacs 2019 -

[ 37%] Built target libgromacs_generated
[ 37%] Built target libgromacs_external
Scanning dependencies of target gpu_utilstest_cuda
[ 37%] Linking CXX shared library ../../../../lib/libgpu_utilstest_cuda.so
[ 37%] Built target gpu_utilstest_cuda

in gromacs 2020-
[ 27%] Built target linearalgebra
[ 27%] Built target scanner
[ 27%] Built target tng_io_obj
[ 27%] Built target modularsimulator

It just stuck on the line and doesn't continue to run.

Any suggestions will be appreciated.
Thanks in advance.


--
Netaly
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Re: [gmx-users] Fatal error pdb2gmx

2020-04-26 Thread Justin Lemkul 




On 4/26/20 5:15 AM, Paolo Costa wrote:

Dear Gromax users,

I created a new residue of 118 atoms within Amber99 force field. However
when I run the "pdb2gmx" I got many times the following warning: "*WARNING:
Duplicate line found in or between hackblock and rtp entries" *and in the
end I got the following fatal error: "*Atom O10 in residue POM 0 was not
found in rtp entry POM with 118 atoms while sorting atoms*". I have no idea
what the warning means, however I do not understand the fatal error since I
am sure that the Atom O1 is present in the residue I created. In attachment
you can find the .pdb and the .rtp files I created.


The mailing list does not accept attachments. If you want to share 
files, upload them to a file-sharing service and provide a link. Note 
that the error mentions O10, not O1.


-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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] Fatal error pdb2gmx

2020-04-26 Thread Paolo Costa 
Dear Gromax users,

I created a new residue of 118 atoms within Amber99 force field. However
when I run the "pdb2gmx" I got many times the following warning: "*WARNING:
Duplicate line found in or between hackblock and rtp entries" *and in the
end I got the following fatal error: "*Atom O10 in residue POM 0 was not
found in rtp entry POM with 118 atoms while sorting atoms*". I have no idea
what the warning means, however I do not understand the fatal error since I
am sure that the Atom O1 is present in the residue I created. In attachment
you can find the .pdb and the .rtp files I created.

Please, can somebody figure out what cause such errors?

Thanks a lot.


Paolo Costa, Ph.D.
Postdoctoral Researcher
Department of Chemistry and Biomolecular Sciences
University of Ottawa
10 Marie Curie, Ottawa, ON K1N 6N5, Canada
Room number: DRO 326 (D'Iorio Hall)
-- 
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[gmx-users] gromacs installation (2020&2019)

2020-04-26 Thread Netaly Khazanov 
Dear All,
I am trying to install gromacs 2020 and 2019 versions on CentOS release
6.10 (Final) linux system.
I passed throuht cmake compilation. Using command
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on
-DCMAKE_INSTALL_PREFIX=gromacs2020
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.0 -DGMX_FFT_LIBRARY=fftw3
-DCMAKE_C_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/cc
-DCMAKE_CXX_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++
-DCUDA_HOST_COMPILER=/opt/rh/devtoolset-6/root/usr/bin/g++
I've used gcc 5 version (tried also 6 version)

However, I am struggling through make execution :
in gromacs 2019 -

[ 37%] Built target libgromacs_generated
[ 37%] Built target libgromacs_external
Scanning dependencies of target gpu_utilstest_cuda
[ 37%] Linking CXX shared library ../../../../lib/libgpu_utilstest_cuda.so
[ 37%] Built target gpu_utilstest_cuda

in gromacs 2020-
[ 27%] Built target linearalgebra
[ 27%] Built target scanner
[ 27%] Built target tng_io_obj
[ 27%] Built target modularsimulator

It just stuck on the line and doesn't continue to run.

Any suggestions will be appreciated.
Thanks in advance.


-- 
Netaly
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