Re: [gmx-users] acpype

[Alan]

We are working on it now. I can't tell you exactly because we need several
tests. It's a complete new version re-written from scratch.

I'm really sorry for the inconvenience but we hope to bring it back in a
month or two.

Alan

On Wed, 24 Oct 2018 at 16:58, neelam wafa  wrote:

> Hi alan
>
> Can you please tell how long will it take for the online acpype server to
> be available?
>
> Regards
> Neelam wafa
>
> On Wed, 24 Oct 2018, 6:23 pm Alan,  wrote:
>
> > Indeed, it's mostly Luciano spearheading these new things. Hopefully, we
> > will have more things to show eventually.
> >
> > Alan
> >
> > On Wed, 24 Oct 2018 at 14:14, Bhupendra Dandekar <
> > bhupendra.dandekar...@gmail.com> wrote:
> >
> > > I actually got lot of help from Luciano Kagami about installation and
> > usage
> > > of acpype and ligro.
> > > Thanks to both of you.
> > >
> > > Bhupendra
> > >
> > > On Wed, Oct 24, 2018 at 6:38 PM Bhupendra Dandekar <
> > > bhupendra.dandekar...@gmail.com> wrote:
> > >
> > > > Thanks to you also sir.
> > > > Your work is really appreciated and is really helpful.
> > > >
> > > >
> > > > Bhupendra
> > > >
> > > > On Wed, Oct 24, 2018 at 3:59 PM Alan  wrote:
> > > >
> > > >> Thanks Bhupendra, indeed we have this option, which is experimental,
> > but
> > > >> I'm glad to see some are already using it and it seems to be
> working.
> > > >>
> > > >> Alan
> > > >>
> > > >> On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar <
> > > >> bhupendra.dandekar...@gmail.com> wrote:
> > > >>
> > > >> > Dear Farial,
> > > >> >
> > > >> > Use this command to install acpype and antechamber using conda:
> > > >> >
> > > >> > conda install -c acpype -c openbabel -c ambermd
> > > >> >
> > > >> > and then you can check and call acpype, antechamber like this from
> > > your
> > > >> > terminal:
> > > >> >
> > > >> > acpype -h
> > > >> > antechamber -h
> > > >> >
> > > >> > then you can generate ligand topology using this command:
> > > >> >
> > > >> > acpype -i FFF.pdb -b FFF -o gmx
> > > >> >
> > > >> > Hope this helps. Let me know if you have any questions.
> > > >> >
> > > >> > Thanks
> > > >> > Bhupendra
> > > >> >
> > > >> > On Wed, Oct 24, 2018 at 2:01 PM Farial Tavakoli <
> > > >> faryal.tavak...@gmail.com
> > > >> > >
> > > >> > wrote:
> > > >> >
> > > >> > > Dear GMX useres
> > > >> > >
> > > >> > > I am trying to convert .OFF and .FRCMOD files obtained from
> AMBER
> > > >> > parameter
> > > >> > > database (Bryce Group: Computational Biophysics and Drug Design
> -
> > > >> > > University of Manchester)
> > > >> > >  to the
> > format
> > > >> that
> > > >> > > GROMACS is compatible with in .rtp files*. so referred to
> GROMACS
> > > >> > tutorial
> > > >> > > protein-ligand complex and downloaded acpype. installed it using
> > its
> > > >> > > readme.txt file but whenever i typed../acpype.py -i FFF.pdb
> >  At
> > > >> > folder
> > > >> > > *acpype/test*   (/Downloads/acpype-master/acpype) or
> > > >> > > (/Downloads/acpype-master/acpype/test) faced to this error:*
> > > >> > >
> > > >> > >
> > > >> > > *bash: ../acpype.py: No such file or directory*
> > > >> > >
> > > >> > > *while when I typed whereis acpype in terminal , the operating
> > > system
> > > >> > says
> > > >> > > :*
> > > >> > >
> > > >> > >
> > > >> > > *acpype: /usr/local/bin/acpype*
> > > >> > > * it means there is the executable file of acpype . so how come
> I
> > > type
> > > >> > > ../acpype.py -h or ../acpype -i FFF.pdb , the system says NO
> such
> > > >> file or
> > > >> > > directory?*
> > > >> > > *Is there anyone who ca help me?*
> > > >> > > *I really would be appreciated it if one help me to solve this
> and
> > > can
> > > >> > > convert the AMBER format files to GRMACS format files.*
> > > >> > >
> > > >> > > *best regards*
> > > >> > > *Farial*
> > > >> > > --
> > > >> > > 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
> > > >> >
> > > >> > * 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.
> > > >> >
> > > >>
> > > >>
> > > >> --
> > > >> *I**​ have just cycled* from Land's End to John O'Groats​​​ (the
> > > >> whole 

Re: [gmx-users] How to generate a new xtc file with a membrane protein complex properly oriented along a given axis?

[Dallas Warren]

Haven't tried it, but seems to me you generate a .tpr file with the
protein orientated correctly within the box, then use trjconv -fit

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Wed, 24 Oct 2018 at 20:38, ABEL Stephane  wrote:
>
> Hello All,
>
> I have  basic questions regarding the procedure to generate an new xtc where 
> a membrane protein inserted a detergent micelle is properly oriented for the 
> computation of 2D density Map. Indeed for this calculation I need to have the 
> protein-surfactant complex properly oriented along a given axis (say Z). For 
> this I chose two atoms and define a vector in my protein and I would like 
> that this vector // to z axis. How to this in GROMACS? I think that editconf 
> can do the trick, however I notice that this tool cannot use and output an 
> xtc file. So is there an alternative approach ? If yes how (an example of 
> command line will be very useful)
>
> Thanks in advance
>
> Stephane
> --
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Re: [gmx-users] Adding residue to .rtp file

[Raji]

Thank you for your reply. I have few more questions
1. Yes, command pdb2gmx continued and generated the topology. The warning
is about 74 atoms which are from the new added rtp entry. I just want to
understand more about the warning. I dont find any related information?
2. What is the significance of the atom types in the rtp file?
for example
CTL3 - carbon of methyl group
CG331 - Aliphatic C for methyl group
What is the difference between them and How to choose the right one for
carbon in alkyl chain?


Thanks
Raji


>
>
> Message: 1
> Date: Fri, 19 Oct 2018 18:32:23 -0400
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Adding residue to .rtp file
> Message-ID: 
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 10/18/18 11:45 AM, Raji wrote:
> > Hi,
> >
> > I have added the modified residue entry in the rtp file and able to
> > generate to topology and .gro file. but i got this warning when passing
> the
> > pdb2gmx command.What is this about?
> > "WARNING: there were 74 atoms with zero occupancy and 0 atoms with
> >   occupancy unequal to one (out of 160 atoms). Check your pdb
> file."
>
> That warning should not present a problem and pdb2gmx should continue.
>
> -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.thelemkullab.com
>
> ==
>
>
> ***
>
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Re: [gmx-users] parameters for plotting 2D density map with gmx densmap and xpm2ps

[Wenjuan Jiang]

Hi  Stéphane

I am interested in the lipid density around the protein, so I only choose
the lipid bilayer to plot 2D density map.

Regarding the coordinates, I need to remove the pbc box effect by 'pbc mol'
of trajconv function so that the protein will be complete, or in Amber,
cpptraj with autoimage function, and this will not affect the function of
densmap and xpm2ps. The 2D without pbc will look like pieces of protein. In
this sense, I think yes, you need to do preprocessing before 2D densemap

Best,
Wenjuan

On Wed, Oct 24, 2018 at 1:21 AM ABEL Stephane  wrote:

> Hi Wenjuan,
>
> Thank you for response is it useful. I have an additional question, did
> you plot in the same xpm figure the 2D dens profiles for the protein and
> the lipids (since I suppose you simulated in a membrane)?
>
> An additional comment, here
> Since your channel was simulated in a bilayer you used the  xtc generated
> during the MD without coordinate manipulations (correct ?). In my case, the
> MP is inserted in a micelle and thus the MP detergent complex can freely
> rotate move during the MD so I need to reorient the complex according the z
> axis "before" to use gmx densmap, correct ?
>
> Thanks you
>
> Stéphane
>
> --
>
> Message: 5
> Date: Tue, 23 Oct 2018 23:31:22 -0700
> From: Wenjuan Jiang 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] parameters for plotting 2D density map with
> gmx densmap and xpm2ps
> Message-ID:
>  sprhaa8...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello  St?phane,
>
> I happened to use densmap and xpm these days for my ion channel.
>
> Here is an example that you can play with for your system.
>
> gmx densmap -f md.xtc -s md.tpr -n index.ndx -aver z -bin 0.05 -dmin 0
> -dmax 20 -unit nm-2 -o md.xpm
> ( later choose the group you are interested in)
>
> -aver z means we want to get top view, that is going to show your dense map
> in xy plane.
> -bin width, you can play with it to get best view.  more options, you can
> check with densmap -h
>
> gmx xmp2ps -f md.xpm -o md.eps -rainbow blue
>
> eps file can be opened either by eps viewer or photoshop.
>
> Thanks,
> Best
> Wenjuan
>
>
> On Tue, Oct 23, 2018 at 7:49 AM ABEL Stephane 
> wrote:
>
> > Dear all,
> >
> > I would like to obtain a 2D density map plot as for instance Fig. 4 in
> the
> > following paper (DOI 10.1007/s00232-014-9690-8) for a membrane protein
> > inserted in a surfactant micelle with gmx densmap and xpm2ps .  I have
> few
> > questions
> >
> > - Have any of you ever done this type of plot? If yes, how?
> > - What parameters for densmap and/or xpm2ps did you use?
> > - How did you combine the protein and surfactant xpm files into a single
> > one to obtain the same plot as Fig. 4
> >
> > Thanks in advance for your help
> >
> > St?phane
> > --
> > 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.
> >
>
>
> --
> Best regards
>
> Wenjuan Jiang
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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>


-- 
Best regards

Wenjuan Jiang
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[gmx-users] Simulated tempering

[Gregory Man Kai Poon]

Hi all,

I am attempting to do simulated tempering on GROMACS 2016.3.  In my 
preliminary googling, I have found several questions from different 
people on the procedure in the past few years but unfortunately without 
response.  I have read up on the literature on the few papers that 
described ST with GROMACS, but have not had much success with the 
authors.  From studying the mdp options, it appears that ST is handled 
under the general umbrella of expanded ensemble simulations.  I am 
therefore hopeful that I could learn from those of you who may not be 
doing ST, but are using related mdp options and are willing to help me out.

Specifically, I am looking for how to extract the updated weights used 
to determine the Metropolis transitions in the MC moves.  I can get 
information such as temperature and lambda in gmx energy, and 
kinetic/potential energy and dH from the output md.xvg.  I've looked in 
md.log.  However, I can't find where the weights are stored.

I would also be thankful for any links on ST with GROMACS that I have 
missed.

Best wishes,

Gregory


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Re: [gmx-users] acpype

[neelam wafa]

Hi alan

Can you please tell how long will it take for the online acpype server to
be available?

Regards
Neelam wafa

On Wed, 24 Oct 2018, 6:23 pm Alan,  wrote:

> Indeed, it's mostly Luciano spearheading these new things. Hopefully, we
> will have more things to show eventually.
>
> Alan
>
> On Wed, 24 Oct 2018 at 14:14, Bhupendra Dandekar <
> bhupendra.dandekar...@gmail.com> wrote:
>
> > I actually got lot of help from Luciano Kagami about installation and
> usage
> > of acpype and ligro.
> > Thanks to both of you.
> >
> > Bhupendra
> >
> > On Wed, Oct 24, 2018 at 6:38 PM Bhupendra Dandekar <
> > bhupendra.dandekar...@gmail.com> wrote:
> >
> > > Thanks to you also sir.
> > > Your work is really appreciated and is really helpful.
> > >
> > >
> > > Bhupendra
> > >
> > > On Wed, Oct 24, 2018 at 3:59 PM Alan  wrote:
> > >
> > >> Thanks Bhupendra, indeed we have this option, which is experimental,
> but
> > >> I'm glad to see some are already using it and it seems to be working.
> > >>
> > >> Alan
> > >>
> > >> On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar <
> > >> bhupendra.dandekar...@gmail.com> wrote:
> > >>
> > >> > Dear Farial,
> > >> >
> > >> > Use this command to install acpype and antechamber using conda:
> > >> >
> > >> > conda install -c acpype -c openbabel -c ambermd
> > >> >
> > >> > and then you can check and call acpype, antechamber like this from
> > your
> > >> > terminal:
> > >> >
> > >> > acpype -h
> > >> > antechamber -h
> > >> >
> > >> > then you can generate ligand topology using this command:
> > >> >
> > >> > acpype -i FFF.pdb -b FFF -o gmx
> > >> >
> > >> > Hope this helps. Let me know if you have any questions.
> > >> >
> > >> > Thanks
> > >> > Bhupendra
> > >> >
> > >> > On Wed, Oct 24, 2018 at 2:01 PM Farial Tavakoli <
> > >> faryal.tavak...@gmail.com
> > >> > >
> > >> > wrote:
> > >> >
> > >> > > Dear GMX useres
> > >> > >
> > >> > > I am trying to convert .OFF and .FRCMOD files obtained from AMBER
> > >> > parameter
> > >> > > database (Bryce Group: Computational Biophysics and Drug Design -
> > >> > > University of Manchester)
> > >> > >  to the
> format
> > >> that
> > >> > > GROMACS is compatible with in .rtp files*. so referred to GROMACS
> > >> > tutorial
> > >> > > protein-ligand complex and downloaded acpype. installed it using
> its
> > >> > > readme.txt file but whenever i typed../acpype.py -i FFF.pdb
>  At
> > >> > folder
> > >> > > *acpype/test*   (/Downloads/acpype-master/acpype) or
> > >> > > (/Downloads/acpype-master/acpype/test) faced to this error:*
> > >> > >
> > >> > >
> > >> > > *bash: ../acpype.py: No such file or directory*
> > >> > >
> > >> > > *while when I typed whereis acpype in terminal , the operating
> > system
> > >> > says
> > >> > > :*
> > >> > >
> > >> > >
> > >> > > *acpype: /usr/local/bin/acpype*
> > >> > > * it means there is the executable file of acpype . so how come I
> > type
> > >> > > ../acpype.py -h or ../acpype -i FFF.pdb , the system says NO such
> > >> file or
> > >> > > directory?*
> > >> > > *Is there anyone who ca help me?*
> > >> > > *I really would be appreciated it if one help me to solve this and
> > can
> > >> > > convert the AMBER format files to GRMACS format files.*
> > >> > >
> > >> > > *best regards*
> > >> > > *Farial*
> > >> > > --
> > >> > > 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.
> > >> >
> > >>
> > >>
> > >> --
> > >> *I**​ have just cycled* from Land's End to John O'Groats​​​ (the
> > >> whole Britain!)
> > >> for a charity, would you consider​ ​supporting my​ cause?
> > >> http://uk.virginmoneygiving.com/AlanSilva
> > >> --
> > >> Alan Wilter SOUSA da SILVA, DSc
> > >> Senior Bioinformatician, UniProt
> > >> European Bioinformatics Institute (EMBL-EBI)
> > >> European Molecular Biology Laboratory
> > >> Wellcome Trust Genome Campus
> > >> Hinxton
> > >> Cambridge CB10 1SD
> > >> United Kingdom
> > >> Tel: +44 (0)1223 494588
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at
> > >> 

[gmx-users] acpype

[farial tavakoli]

Dear Justin
I installed acpype on the ubuntu but didnt install Antechamber and openbable . 
Now I am trying to convert the AMBER parameters format (obtained from 
http://sites.pharmacy.manchester.ac.uk/bryce/amber  ) to the one that gromacs 
is compatible with in the .rtp files. I pasted acpype.py in the directory that 
I am working and issued this command:
python acpype.py -i XXX.pdb 
but faced to this error:
ERROR: no 'antechamber' executable!
ERROR: no 'antechamber' executable... aborting ! 
==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?
==> HINT2: is 'antechamber' in your $PATH?
    What 'which antechamber' in your terminal says?
    'alias' doesn't work for ACPYPE.
ACPYPE FAILED: 1
Total time of execution: less than a second

while I read in the readme.txt file of acpype and in google that ' However, if 
one wants *acpype* just to emulate *amb2gmx.pl*, one needs nothing at all but 
*[http://www.python.org Python]*.'  or  'ACPYPE is far better than amb2gmx.pl 
and won't even need AmberTools if you
just want to covert Amber topology to GMX'.
 I can not understand where the problem is? 
I would be appreciated it if you help me
thanks in advanceFarial

 


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Re: [gmx-users] acpype

[Alan]

Indeed, it's mostly Luciano spearheading these new things. Hopefully, we
will have more things to show eventually.

Alan

On Wed, 24 Oct 2018 at 14:14, Bhupendra Dandekar <
bhupendra.dandekar...@gmail.com> wrote:

> I actually got lot of help from Luciano Kagami about installation and usage
> of acpype and ligro.
> Thanks to both of you.
>
> Bhupendra
>
> On Wed, Oct 24, 2018 at 6:38 PM Bhupendra Dandekar <
> bhupendra.dandekar...@gmail.com> wrote:
>
> > Thanks to you also sir.
> > Your work is really appreciated and is really helpful.
> >
> >
> > Bhupendra
> >
> > On Wed, Oct 24, 2018 at 3:59 PM Alan  wrote:
> >
> >> Thanks Bhupendra, indeed we have this option, which is experimental, but
> >> I'm glad to see some are already using it and it seems to be working.
> >>
> >> Alan
> >>
> >> On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar <
> >> bhupendra.dandekar...@gmail.com> wrote:
> >>
> >> > Dear Farial,
> >> >
> >> > Use this command to install acpype and antechamber using conda:
> >> >
> >> > conda install -c acpype -c openbabel -c ambermd
> >> >
> >> > and then you can check and call acpype, antechamber like this from
> your
> >> > terminal:
> >> >
> >> > acpype -h
> >> > antechamber -h
> >> >
> >> > then you can generate ligand topology using this command:
> >> >
> >> > acpype -i FFF.pdb -b FFF -o gmx
> >> >
> >> > Hope this helps. Let me know if you have any questions.
> >> >
> >> > Thanks
> >> > Bhupendra
> >> >
> >> > On Wed, Oct 24, 2018 at 2:01 PM Farial Tavakoli <
> >> faryal.tavak...@gmail.com
> >> > >
> >> > wrote:
> >> >
> >> > > Dear GMX useres
> >> > >
> >> > > I am trying to convert .OFF and .FRCMOD files obtained from AMBER
> >> > parameter
> >> > > database (Bryce Group: Computational Biophysics and Drug Design -
> >> > > University of Manchester)
> >> > >  to the format
> >> that
> >> > > GROMACS is compatible with in .rtp files*. so referred to GROMACS
> >> > tutorial
> >> > > protein-ligand complex and downloaded acpype. installed it using its
> >> > > readme.txt file but whenever i typed../acpype.py -i FFF.pdb   At
> >> > folder
> >> > > *acpype/test*   (/Downloads/acpype-master/acpype) or
> >> > > (/Downloads/acpype-master/acpype/test) faced to this error:*
> >> > >
> >> > >
> >> > > *bash: ../acpype.py: No such file or directory*
> >> > >
> >> > > *while when I typed whereis acpype in terminal , the operating
> system
> >> > says
> >> > > :*
> >> > >
> >> > >
> >> > > *acpype: /usr/local/bin/acpype*
> >> > > * it means there is the executable file of acpype . so how come I
> type
> >> > > ../acpype.py -h or ../acpype -i FFF.pdb , the system says NO such
> >> file or
> >> > > directory?*
> >> > > *Is there anyone who ca help me?*
> >> > > *I really would be appreciated it if one help me to solve this and
> can
> >> > > convert the AMBER format files to GRMACS format files.*
> >> > >
> >> > > *best regards*
> >> > > *Farial*
> >> > > --
> >> > > 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
> >> >
> >> > * 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.
> >> >
> >>
> >>
> >> --
> >> *I**​ have just cycled* from Land's End to John O'Groats​​​ (the
> >> whole Britain!)
> >> for a charity, would you consider​ ​supporting my​ cause?
> >> http://uk.virginmoneygiving.com/AlanSilva
> >> --
> >> Alan Wilter SOUSA da SILVA, DSc
> >> Senior Bioinformatician, UniProt
> >> European Bioinformatics Institute (EMBL-EBI)
> >> European Molecular Biology Laboratory
> >> Wellcome Trust Genome Campus
> >> Hinxton
> >> Cambridge CB10 1SD
> >> United Kingdom
> >> Tel: +44 (0)1223 494588
> >> --
> >> 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 

Re: [gmx-users] acpype

[Bhupendra Dandekar]

I actually got lot of help from Luciano Kagami about installation and usage
of acpype and ligro.
Thanks to both of you.

Bhupendra

On Wed, Oct 24, 2018 at 6:38 PM Bhupendra Dandekar <
bhupendra.dandekar...@gmail.com> wrote:

> Thanks to you also sir.
> Your work is really appreciated and is really helpful.
>
>
> Bhupendra
>
> On Wed, Oct 24, 2018 at 3:59 PM Alan  wrote:
>
>> Thanks Bhupendra, indeed we have this option, which is experimental, but
>> I'm glad to see some are already using it and it seems to be working.
>>
>> Alan
>>
>> On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar <
>> bhupendra.dandekar...@gmail.com> wrote:
>>
>> > Dear Farial,
>> >
>> > Use this command to install acpype and antechamber using conda:
>> >
>> > conda install -c acpype -c openbabel -c ambermd
>> >
>> > and then you can check and call acpype, antechamber like this from your
>> > terminal:
>> >
>> > acpype -h
>> > antechamber -h
>> >
>> > then you can generate ligand topology using this command:
>> >
>> > acpype -i FFF.pdb -b FFF -o gmx
>> >
>> > Hope this helps. Let me know if you have any questions.
>> >
>> > Thanks
>> > Bhupendra
>> >
>> > On Wed, Oct 24, 2018 at 2:01 PM Farial Tavakoli <
>> faryal.tavak...@gmail.com
>> > >
>> > wrote:
>> >
>> > > Dear GMX useres
>> > >
>> > > I am trying to convert .OFF and .FRCMOD files obtained from AMBER
>> > parameter
>> > > database (Bryce Group: Computational Biophysics and Drug Design -
>> > > University of Manchester)
>> > >  to the format
>> that
>> > > GROMACS is compatible with in .rtp files*. so referred to GROMACS
>> > tutorial
>> > > protein-ligand complex and downloaded acpype. installed it using its
>> > > readme.txt file but whenever i typed../acpype.py -i FFF.pdb   At
>> > folder
>> > > *acpype/test*   (/Downloads/acpype-master/acpype) or
>> > > (/Downloads/acpype-master/acpype/test) faced to this error:*
>> > >
>> > >
>> > > *bash: ../acpype.py: No such file or directory*
>> > >
>> > > *while when I typed whereis acpype in terminal , the operating system
>> > says
>> > > :*
>> > >
>> > >
>> > > *acpype: /usr/local/bin/acpype*
>> > > * it means there is the executable file of acpype . so how come I type
>> > > ../acpype.py -h or ../acpype -i FFF.pdb , the system says NO such
>> file or
>> > > directory?*
>> > > *Is there anyone who ca help me?*
>> > > *I really would be appreciated it if one help me to solve this and can
>> > > convert the AMBER format files to GRMACS format files.*
>> > >
>> > > *best regards*
>> > > *Farial*
>> > > --
>> > > 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
>> >
>> > * 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.
>> >
>>
>>
>> --
>> *I**​ have just cycled* from Land's End to John O'Groats​​​ (the
>> whole Britain!)
>> for a charity, would you consider​ ​supporting my​ cause?
>> http://uk.virginmoneygiving.com/AlanSilva
>> --
>> Alan Wilter SOUSA da SILVA, DSc
>> Senior Bioinformatician, UniProt
>> European Bioinformatics Institute (EMBL-EBI)
>> European Molecular Biology Laboratory
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridge CB10 1SD
>> United Kingdom
>> Tel: +44 (0)1223 494588
>> --
>> 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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Re: [gmx-users] acpype

[Bhupendra Dandekar]

Thanks to you also sir.
Your work is really appreciated and is really helpful.


Bhupendra

On Wed, Oct 24, 2018 at 3:59 PM Alan  wrote:

> Thanks Bhupendra, indeed we have this option, which is experimental, but
> I'm glad to see some are already using it and it seems to be working.
>
> Alan
>
> On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar <
> bhupendra.dandekar...@gmail.com> wrote:
>
> > Dear Farial,
> >
> > Use this command to install acpype and antechamber using conda:
> >
> > conda install -c acpype -c openbabel -c ambermd
> >
> > and then you can check and call acpype, antechamber like this from your
> > terminal:
> >
> > acpype -h
> > antechamber -h
> >
> > then you can generate ligand topology using this command:
> >
> > acpype -i FFF.pdb -b FFF -o gmx
> >
> > Hope this helps. Let me know if you have any questions.
> >
> > Thanks
> > Bhupendra
> >
> > On Wed, Oct 24, 2018 at 2:01 PM Farial Tavakoli <
> faryal.tavak...@gmail.com
> > >
> > wrote:
> >
> > > Dear GMX useres
> > >
> > > I am trying to convert .OFF and .FRCMOD files obtained from AMBER
> > parameter
> > > database (Bryce Group: Computational Biophysics and Drug Design -
> > > University of Manchester)
> > >  to the format
> that
> > > GROMACS is compatible with in .rtp files*. so referred to GROMACS
> > tutorial
> > > protein-ligand complex and downloaded acpype. installed it using its
> > > readme.txt file but whenever i typed../acpype.py -i FFF.pdb   At
> > folder
> > > *acpype/test*   (/Downloads/acpype-master/acpype) or
> > > (/Downloads/acpype-master/acpype/test) faced to this error:*
> > >
> > >
> > > *bash: ../acpype.py: No such file or directory*
> > >
> > > *while when I typed whereis acpype in terminal , the operating system
> > says
> > > :*
> > >
> > >
> > > *acpype: /usr/local/bin/acpype*
> > > * it means there is the executable file of acpype . so how come I type
> > > ../acpype.py -h or ../acpype -i FFF.pdb , the system says NO such file
> or
> > > directory?*
> > > *Is there anyone who ca help me?*
> > > *I really would be appreciated it if one help me to solve this and can
> > > convert the AMBER format files to GRMACS format files.*
> > >
> > > *best regards*
> > > *Farial*
> > > --
> > > 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
> >
> > * 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.
> >
>
>
> --
> *I**​ have just cycled* from Land's End to John O'Groats​​​ (the
> whole Britain!)
> for a charity, would you consider​ ​supporting my​ cause?
> http://uk.virginmoneygiving.com/AlanSilva
> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: +44 (0)1223 494588
> --
> 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 
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Re: [gmx-users] gmx kill computer?

[Wahab Mirco]

On 24.10.2018 11:07, Michael Brunsteiner wrote:
> Harry and Mirco!I've got 700W Thermaltake PSUs here ... according to several 
> web-sites thatcalculate the expected power consumption for a given set of 
> components, and alsoin our experience this should be more than enough ...Can 
> it be that, as Mirco suggested, the 1060 in combination with gmx can give 
> particularlylarge spikes or changes in energy consumption so that even a 700W 
> PSU cannot cope?
> 

What PSU model exactly and from when? Do both machines do have exactly 
the same type of PSU?

M.
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Re: [gmx-users] nvcc fatal: 'avx512f': expected a number

[Mark Abraham]

Hi,

On Wed, Oct 24, 2018 at 11:50 AM Ehsan Moravveji 
wrote:

> Dear Mark,
>
> Sincere thanks for your swift reply, and apologies for the duplicate
> message; I realized that my original message had no subject, so, I thought
> it is more proper to send the message with a meaningful topic;
>

OK


> Regarding your comment, I am building GROMACS from source, and without
> intervention from EasyBuild. In order to be transparent, I also put my full
> cmake command arguments in the original message as well. Since some other
> dependencies are installed by EasyBuild as modules, I am setting some of
> the paths in a compatible way on our system, hence e.g. EBROOTCUDA, etc.
>

Then you will have a easier time if you start with a simple invocation,
rather than manually configuring a whole host of things, including CUDA
flags. If e.g. those flags are wrongly escaped for the different wrappers,
then you will get mysterious issues like this :-) So I suggest you start
with

cmake -DGMX_SIMD=AVX_512 -DCUDA_TOOLKIT_ROOT_DIR=whatever

and gradually add the complexity that you think is needed (e.g. MKL, MPI,
NVML...)

To double check your feedback, let me ask the following:
> I am explicitly setting the flag -DGMX_SIMD='AVX_512'. Is it equivalent to
>

That's a GROMACS cmake flag.


> the flag you proposed (-mavx512f), or I have to add the latter to the
>

That's a flag for the compiler. They're not the same. But when the GROMACS
build tries to target AVX512, it checks what flags works and organizes to
use them. I assume that the way you're adding things manually to the CUDA
flags is breaking e.g. the tricks that FindCUDA.cmake has to do in order to
invoke the CUDA compiler.

Mark


> argument list to cmake, too?
>
> Sincere thanks,
> Ehsan
>
>
> On Wed, Oct 24, 2018 at 10:42 AM Mark Abraham 
> wrote:
>
> > Hi,
> >
> > You sent this email yesterday. Please be a little more patient.
> >
> > Unfortunately, I have no idea how EasyBuild works, and suspect that the
> > problem lies in the way it is wrapping arguments that then get passed to
> > nvcc. If you can reproduce this issue with a simple call to cmake with
> > minimal extra stuff, then we can explore whether there's an issue with
> the
> > GROMACS build system. But since -mavx512f is a valid compiler flag that
> > GROMACS checked was valid before using it, I suspect the problem isn't
> > ours.
> >
> > Mark
> >
> > On Wed, Oct 24, 2018 at 9:55 AM Ehsan Moravveji 
> > wrote:
> >
> > > Dear GMX users,
> > >
> > > I would like to share a difficulty installing GROMACS/2018.3 with you,
> > > and kindly ask for your wisdom.
> > >
> > > I use GCC/6.4.0 on a Linux cluster with CentOS 7.5 kernel and GPU
> > > nodes equipped with 4 x P100 Nvidia devices.
> > >
> > >
> > > Below is the cmake configuration that I use, followed by the error (in
> > > boldface font) that I
> > > receive. I am not sure if there is still an extra flag to set to
> resolve
> > > this issue, or some other steps must be taken?
> > >
> > > I appreciate your input.
> > >
> > > --
> > > Kind regards,
> > > Ehsan Moravveji
> > >
> > > ###
> > > cmake "${cwd}/${dir_src}" \
> > >   -DGMX_SIMD='AVX_512' \
> > >   -DBLAS_mkl_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \
> > >   -DLAPACK_mkl_lapack_LIBRARY="DIR_MKL_LIB/libmkl_sequential.so" \
> > >   -DBLAS_guide_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \
> > >   -DCMAKE_C_COMPILER="${GMX_MPICC}"
> -DCMAKE_CXX_COMPILER="${GMX_MPICXX}"
> > \
> > >   -DMPI_C_COMPILER="${GMX_MPICC}" -DMPI_CXX_COMPILER="${GMX_MPICXX}" \
> > >   -DCMAKE_MPI_C_COMPILER="${GMX_MPICC}"
> > > -DCMAKE_MPI_CXX_COMPILER="${GMX_MPICXX}" \
> > >   -DCMAKE_INSTALL_PREFIX="${dir_install}" \
> > >   -DCMAKE_PREFIX_PATH="${DIR_MKL_LIB}" \
> > >   -DCMAKE_VERBOSE_MAKEFILE=ON \
> > >   -DGMX_MPI=ON \
> > >   -DGMX_GPU=ON \
> > >   -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF -DEXTRA_CXX_FLAGS="-std=c++11" \
> > >   -DGMX_USE_NVML=ON -DGMX_BUILD_OWN_FFTW=ON \
> > >   -DHWLOC_INCLUDE_DIRS="${EBROOTHWLOC}/include"
> > > -DHWLOC_LIBRARIES="${EBROOTHWLOC}/lib/libhwloc.so" \
> > >   -DCUDA_HOST_COMPILER="${PATH_NVCC}"
> > > -DNVML_INCLUDE_DIR="${EBROOTCUDA}/include" \
> > >   -DNVML_LIBRARY="${EBROOTCUDA}/lib64/stubs/libnvidia-ml.so" \
> > >   -DCUDA_TOOLKIT_ROOT_DIR="${EBROOTCUDA}"
> > > -DCUDA_SDK_ROOT_DIR="${EBROOTCUDA}" \
> > >   -DCUDA_PROPAGATE_HOST_FLAGS=ON -DCUDA_VERBOSE_BUILD=ON \
> > >   -DGMX_CUDA_TARGET_SM="${SM_VER}"
> -DGMX_CUDA_TARGET_COMPUTE="${SM_VER}"
> > \
> > >   -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF \
> > >   -DCUDA_CUDART_LIBRARY="${EBROOTCUDA}/lib64/libcudart.so"
> > > -DCUDA_CUDA_LIBRARY="${EBROOTCUDA}/lib64/libcuda.so" \
> > >
> > >
> > >
> >
> -DCUDA_NVCC_FLAGS="-gencode;arch=compute_${SM_VER},code=compute_${SM_VER};-use_fast_math;-D_FORCE_INLINES"
> > > \
> > >   -DGMX_PREFER_STATIC_LIBS=OFF -DGMX_X11=OFF
> > >
> > > ###
> > >
> > > -- Generating dependency file:
> > >
> > >
> >
> 

Re: [gmx-users] acpype

[Alan]

Thanks Bhupendra, indeed we have this option, which is experimental, but
I'm glad to see some are already using it and it seems to be working.

Alan

On Wed, 24 Oct 2018 at 11:20, Bhupendra Dandekar <
bhupendra.dandekar...@gmail.com> wrote:

> Dear Farial,
>
> Use this command to install acpype and antechamber using conda:
>
> conda install -c acpype -c openbabel -c ambermd
>
> and then you can check and call acpype, antechamber like this from your
> terminal:
>
> acpype -h
> antechamber -h
>
> then you can generate ligand topology using this command:
>
> acpype -i FFF.pdb -b FFF -o gmx
>
> Hope this helps. Let me know if you have any questions.
>
> Thanks
> Bhupendra
>
> On Wed, Oct 24, 2018 at 2:01 PM Farial Tavakoli  >
> wrote:
>
> > Dear GMX useres
> >
> > I am trying to convert .OFF and .FRCMOD files obtained from AMBER
> parameter
> > database (Bryce Group: Computational Biophysics and Drug Design -
> > University of Manchester)
> >  to the format that
> > GROMACS is compatible with in .rtp files*. so referred to GROMACS
> tutorial
> > protein-ligand complex and downloaded acpype. installed it using its
> > readme.txt file but whenever i typed../acpype.py -i FFF.pdb   At
> folder
> > *acpype/test*   (/Downloads/acpype-master/acpype) or
> > (/Downloads/acpype-master/acpype/test) faced to this error:*
> >
> >
> > *bash: ../acpype.py: No such file or directory*
> >
> > *while when I typed whereis acpype in terminal , the operating system
> says
> > :*
> >
> >
> > *acpype: /usr/local/bin/acpype*
> > * it means there is the executable file of acpype . so how come I type
> > ../acpype.py -h or ../acpype -i FFF.pdb , the system says NO such file or
> > directory?*
> > *Is there anyone who ca help me?*
> > *I really would be appreciated it if one help me to solve this and can
> > convert the AMBER format files to GRMACS format files.*
> >
> > *best regards*
> > *Farial*
> > --
> > 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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-- 
*I**​ have just cycled* from Land's End to John O'Groats​​​ (the
whole Britain!)
for a charity, would you consider​ ​supporting my​ cause?
http://uk.virginmoneygiving.com/AlanSilva
--
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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Re: [gmx-users] acpype

[Bhupendra Dandekar]

Dear Farial,

Use this command to install acpype and antechamber using conda:

conda install -c acpype -c openbabel -c ambermd

and then you can check and call acpype, antechamber like this from your
terminal:

acpype -h
antechamber -h

then you can generate ligand topology using this command:

acpype -i FFF.pdb -b FFF -o gmx

Hope this helps. Let me know if you have any questions.

Thanks
Bhupendra

On Wed, Oct 24, 2018 at 2:01 PM Farial Tavakoli 
wrote:

> Dear GMX useres
>
> I am trying to convert .OFF and .FRCMOD files obtained from AMBER parameter
> database (Bryce Group: Computational Biophysics and Drug Design -
> University of Manchester)
>  to the format that
> GROMACS is compatible with in .rtp files*. so referred to GROMACS tutorial
> protein-ligand complex and downloaded acpype. installed it using its
> readme.txt file but whenever i typed../acpype.py -i FFF.pdb   At folder
> *acpype/test*   (/Downloads/acpype-master/acpype) or
> (/Downloads/acpype-master/acpype/test) faced to this error:*
>
>
> *bash: ../acpype.py: No such file or directory*
>
> *while when I typed whereis acpype in terminal , the operating system says
> :*
>
>
> *acpype: /usr/local/bin/acpype*
> * it means there is the executable file of acpype . so how come I type
> ../acpype.py -h or ../acpype -i FFF.pdb , the system says NO such file or
> directory?*
> *Is there anyone who ca help me?*
> *I really would be appreciated it if one help me to solve this and can
> convert the AMBER format files to GRMACS format files.*
>
> *best regards*
> *Farial*
> --
> 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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Re: [gmx-users] nvcc fatal: 'avx512f': expected a number

[Ehsan Moravveji]

Dear Mark,

Sincere thanks for your swift reply, and apologies for the duplicate
message; I realized that my original message had no subject, so, I thought
it is more proper to send the message with a meaningful topic;

Regarding your comment, I am building GROMACS from source, and without
intervention from EasyBuild. In order to be transparent, I also put my full
cmake command arguments in the original message as well. Since some other
dependencies are installed by EasyBuild as modules, I am setting some of
the paths in a compatible way on our system, hence e.g. EBROOTCUDA, etc.

To double check your feedback, let me ask the following:
I am explicitly setting the flag -DGMX_SIMD='AVX_512'. Is it equivalent to
the flag you proposed (-mavx512f), or I have to add the latter to the
argument list to cmake, too?

Sincere thanks,
Ehsan


On Wed, Oct 24, 2018 at 10:42 AM Mark Abraham 
wrote:

> Hi,
>
> You sent this email yesterday. Please be a little more patient.
>
> Unfortunately, I have no idea how EasyBuild works, and suspect that the
> problem lies in the way it is wrapping arguments that then get passed to
> nvcc. If you can reproduce this issue with a simple call to cmake with
> minimal extra stuff, then we can explore whether there's an issue with the
> GROMACS build system. But since -mavx512f is a valid compiler flag that
> GROMACS checked was valid before using it, I suspect the problem isn't
> ours.
>
> Mark
>
> On Wed, Oct 24, 2018 at 9:55 AM Ehsan Moravveji 
> wrote:
>
> > Dear GMX users,
> >
> > I would like to share a difficulty installing GROMACS/2018.3 with you,
> > and kindly ask for your wisdom.
> >
> > I use GCC/6.4.0 on a Linux cluster with CentOS 7.5 kernel and GPU
> > nodes equipped with 4 x P100 Nvidia devices.
> >
> >
> > Below is the cmake configuration that I use, followed by the error (in
> > boldface font) that I
> > receive. I am not sure if there is still an extra flag to set to resolve
> > this issue, or some other steps must be taken?
> >
> > I appreciate your input.
> >
> > --
> > Kind regards,
> > Ehsan Moravveji
> >
> > ###
> > cmake "${cwd}/${dir_src}" \
> >   -DGMX_SIMD='AVX_512' \
> >   -DBLAS_mkl_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \
> >   -DLAPACK_mkl_lapack_LIBRARY="DIR_MKL_LIB/libmkl_sequential.so" \
> >   -DBLAS_guide_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \
> >   -DCMAKE_C_COMPILER="${GMX_MPICC}" -DCMAKE_CXX_COMPILER="${GMX_MPICXX}"
> \
> >   -DMPI_C_COMPILER="${GMX_MPICC}" -DMPI_CXX_COMPILER="${GMX_MPICXX}" \
> >   -DCMAKE_MPI_C_COMPILER="${GMX_MPICC}"
> > -DCMAKE_MPI_CXX_COMPILER="${GMX_MPICXX}" \
> >   -DCMAKE_INSTALL_PREFIX="${dir_install}" \
> >   -DCMAKE_PREFIX_PATH="${DIR_MKL_LIB}" \
> >   -DCMAKE_VERBOSE_MAKEFILE=ON \
> >   -DGMX_MPI=ON \
> >   -DGMX_GPU=ON \
> >   -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF -DEXTRA_CXX_FLAGS="-std=c++11" \
> >   -DGMX_USE_NVML=ON -DGMX_BUILD_OWN_FFTW=ON \
> >   -DHWLOC_INCLUDE_DIRS="${EBROOTHWLOC}/include"
> > -DHWLOC_LIBRARIES="${EBROOTHWLOC}/lib/libhwloc.so" \
> >   -DCUDA_HOST_COMPILER="${PATH_NVCC}"
> > -DNVML_INCLUDE_DIR="${EBROOTCUDA}/include" \
> >   -DNVML_LIBRARY="${EBROOTCUDA}/lib64/stubs/libnvidia-ml.so" \
> >   -DCUDA_TOOLKIT_ROOT_DIR="${EBROOTCUDA}"
> > -DCUDA_SDK_ROOT_DIR="${EBROOTCUDA}" \
> >   -DCUDA_PROPAGATE_HOST_FLAGS=ON -DCUDA_VERBOSE_BUILD=ON \
> >   -DGMX_CUDA_TARGET_SM="${SM_VER}" -DGMX_CUDA_TARGET_COMPUTE="${SM_VER}"
> \
> >   -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF \
> >   -DCUDA_CUDART_LIBRARY="${EBROOTCUDA}/lib64/libcudart.so"
> > -DCUDA_CUDA_LIBRARY="${EBROOTCUDA}/lib64/libcuda.so" \
> >
> >
> >
> -DCUDA_NVCC_FLAGS="-gencode;arch=compute_${SM_VER},code=compute_${SM_VER};-use_fast_math;-D_FORCE_INLINES"
> > \
> >   -DGMX_PREFER_STATIC_LIBS=OFF -DGMX_X11=OFF
> >
> > ###
> >
> > -- Generating dependency file:
> >
> >
> /work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.NVCC-depend
> > /software/CUDA/9.2.148/bin/nvcc -M -D__CUDACC__
> > /work/GROMACS/gromacs-2018.3/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu
> -o
> >
> >
> /work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.NVCC-depend
> > -ccbin /software/CUDA/9.2.148/bin/nvcc -m64 --std
> > c++11 -Dlibgromacs_EXPORTS -DGMX_DOUBLE=0 -DHAVE_CONFIG_H
> > -DUSE_STD_INTTYPES_H -Xcompiler
> >
> >
> ,\"-mavx512f\",\"-mfma\",\"-fPIC\",\"-O3\",\"-DNDEBUG\",\"-funroll-all-loops\",\"-fexcess-precision=fast\"
> > -gencode arch=compute_60,code=sm_60 -gencode
> > arch=compute_60,code=compute_60 -use_fast_math -gencode
> > arch=compute_60,code=compute_60 -use_fast_math -D_FORCE_INLINES -DNVCC
> > -I/software/CUDA/9.2.148/include
> > -I/work/GROMACS/gromacs-2018.3/src/external/lmfit
> >
> >
> -I/work/GROMACS/gromacs-2018.3-build/src/contrib/fftw/fftwBuild-prefix/include
> > -I/work/GROMACS/gromacs-2018.3-build/src
> > 

[gmx-users] How to generate a new xtc file with a membrane protein complex properly oriented along a given axis?

[ABEL Stephane]

Hello All, 

I have  basic questions regarding the procedure to generate an new xtc where a 
membrane protein inserted a detergent micelle is properly oriented for the 
computation of 2D density Map. Indeed for this calculation I need to have the 
protein-surfactant complex properly oriented along a given axis (say Z). For 
this I chose two atoms and define a vector in my protein and I would like that 
this vector // to z axis. How to this in GROMACS? I think that editconf can do 
the trick, however I notice that this tool cannot use and output an xtc file. 
So is there an alternative approach ? If yes how (an example of command line 
will be very useful) 

Thanks in advance

Stephane
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Re: [gmx-users] acpype

[Alan]

Latest acpype is here: https://github.com/alanwilter/acpype

Mind that it's *only* Python 3 compatible now.

Run something like this, at first, to be sure:

_full_to_your_python3 _full_path_to_acpype -d -i ...

You need Antechamber (from Amber) if you want to generate topologies.

Only if converting from Amber to GMX that you do not need Antechamber (but
if you play with AMBER format, you certainly have AmberTools installed,
right?)

I hope it helps,

Alan

On Wed, 24 Oct 2018 at 09:31, Farial Tavakoli 
wrote:

> Dear GMX useres
>
> I am trying to convert .OFF and .FRCMOD files obtained from AMBER parameter
> database (Bryce Group: Computational Biophysics and Drug Design -
> University of Manchester)
>  to the format that
> GROMACS is compatible with in .rtp files*. so referred to GROMACS tutorial
> protein-ligand complex and downloaded acpype. installed it using its
> readme.txt file but whenever i typed../acpype.py -i FFF.pdb   At folder
> *acpype/test*   (/Downloads/acpype-master/acpype) or
> (/Downloads/acpype-master/acpype/test) faced to this error:*
>
>
> *bash: ../acpype.py: No such file or directory*
>
> *while when I typed whereis acpype in terminal , the operating system says
> :*
>
>
> *acpype: /usr/local/bin/acpype*
> * it means there is the executable file of acpype . so how come I type
> ../acpype.py -h or ../acpype -i FFF.pdb , the system says NO such file or
> directory?*
> *Is there anyone who ca help me?*
> *I really would be appreciated it if one help me to solve this and can
> convert the AMBER format files to GRMACS format files.*
>
> *best regards*
> *Farial*
> --
> 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.
>


-- 
*I**​ have just cycled* from Land's End to John O'Groats​​​ (the
whole Britain!)
for a charity, would you consider​ ​supporting my​ cause?
http://uk.virginmoneygiving.com/AlanSilva
--
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
-- 
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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[gmx-users] gmx kill computer?

[Michael Brunsteiner]

Hi, 

Thanks for you replies, Harry and Mirco!I've got 700W Thermaltake PSUs here ... 
according to several web-sites thatcalculate the expected power consumption for 
a given set of components, and alsoin our experience this should be more than 
enough ...Can it be that, as Mirco suggested, the 1060 in combination with gmx 
can give particularlylarge spikes or changes in energy consumption so that even 
a 700W PSU cannot cope?
cheers,michael


>On 23.10.2018 15:12, Michael Brunsteiner wrote:
>> the computers are NOT overclocked, cooling works, cpu temperatures are well 
>> below max.
>> as stated above something like this happened three times, each time with gmx 
>> at full blastand
>> with the same type of nvidia card ... can it be that my hardware has some 
>> issue that isso well
>> hidden that only gromacs running at full blast can trigger it? - has anybody 
>> observedsuch
>> behaviour before, or suggestions on how to better diagnose the issue ... ??
>> 
>> the specs:
>> workstation 1Intel(R) Core(TM) i7-4930K CPU @ 3.40GHz + nvidia geforce gtx 
>> 1060
>> running debian stretch with nvidia driver version 387.26
>> workstation 2AMD Ryzen 7 2700X Eight-Core Processor + nvidia geforce gtx 1060
>> running debian stretch with nvidia driver version 390.87
>GTX-1060, due to the interval-like offloading of gpu-related work will
>possibly generate some really nasty load-changes the power supply can't
>cope with. It is well known that fast load changes of modern graphics
>cards may overstrain the power supply unit if not "strong" enough.
>The symptoms very much suggest a problem with the PSU.






=== Why be happy when you could be normal?
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Re: [gmx-users] nvcc fatal: 'avx512f': expected a number

[Mark Abraham]

Hi,

You sent this email yesterday. Please be a little more patient.

Unfortunately, I have no idea how EasyBuild works, and suspect that the
problem lies in the way it is wrapping arguments that then get passed to
nvcc. If you can reproduce this issue with a simple call to cmake with
minimal extra stuff, then we can explore whether there's an issue with the
GROMACS build system. But since -mavx512f is a valid compiler flag that
GROMACS checked was valid before using it, I suspect the problem isn't ours.

Mark

On Wed, Oct 24, 2018 at 9:55 AM Ehsan Moravveji 
wrote:

> Dear GMX users,
>
> I would like to share a difficulty installing GROMACS/2018.3 with you,
> and kindly ask for your wisdom.
>
> I use GCC/6.4.0 on a Linux cluster with CentOS 7.5 kernel and GPU
> nodes equipped with 4 x P100 Nvidia devices.
>
>
> Below is the cmake configuration that I use, followed by the error (in
> boldface font) that I
> receive. I am not sure if there is still an extra flag to set to resolve
> this issue, or some other steps must be taken?
>
> I appreciate your input.
>
> --
> Kind regards,
> Ehsan Moravveji
>
> ###
> cmake "${cwd}/${dir_src}" \
>   -DGMX_SIMD='AVX_512' \
>   -DBLAS_mkl_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \
>   -DLAPACK_mkl_lapack_LIBRARY="DIR_MKL_LIB/libmkl_sequential.so" \
>   -DBLAS_guide_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \
>   -DCMAKE_C_COMPILER="${GMX_MPICC}" -DCMAKE_CXX_COMPILER="${GMX_MPICXX}" \
>   -DMPI_C_COMPILER="${GMX_MPICC}" -DMPI_CXX_COMPILER="${GMX_MPICXX}" \
>   -DCMAKE_MPI_C_COMPILER="${GMX_MPICC}"
> -DCMAKE_MPI_CXX_COMPILER="${GMX_MPICXX}" \
>   -DCMAKE_INSTALL_PREFIX="${dir_install}" \
>   -DCMAKE_PREFIX_PATH="${DIR_MKL_LIB}" \
>   -DCMAKE_VERBOSE_MAKEFILE=ON \
>   -DGMX_MPI=ON \
>   -DGMX_GPU=ON \
>   -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF -DEXTRA_CXX_FLAGS="-std=c++11" \
>   -DGMX_USE_NVML=ON -DGMX_BUILD_OWN_FFTW=ON \
>   -DHWLOC_INCLUDE_DIRS="${EBROOTHWLOC}/include"
> -DHWLOC_LIBRARIES="${EBROOTHWLOC}/lib/libhwloc.so" \
>   -DCUDA_HOST_COMPILER="${PATH_NVCC}"
> -DNVML_INCLUDE_DIR="${EBROOTCUDA}/include" \
>   -DNVML_LIBRARY="${EBROOTCUDA}/lib64/stubs/libnvidia-ml.so" \
>   -DCUDA_TOOLKIT_ROOT_DIR="${EBROOTCUDA}"
> -DCUDA_SDK_ROOT_DIR="${EBROOTCUDA}" \
>   -DCUDA_PROPAGATE_HOST_FLAGS=ON -DCUDA_VERBOSE_BUILD=ON \
>   -DGMX_CUDA_TARGET_SM="${SM_VER}" -DGMX_CUDA_TARGET_COMPUTE="${SM_VER}" \
>   -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF \
>   -DCUDA_CUDART_LIBRARY="${EBROOTCUDA}/lib64/libcudart.so"
> -DCUDA_CUDA_LIBRARY="${EBROOTCUDA}/lib64/libcuda.so" \
>
>
> -DCUDA_NVCC_FLAGS="-gencode;arch=compute_${SM_VER},code=compute_${SM_VER};-use_fast_math;-D_FORCE_INLINES"
> \
>   -DGMX_PREFER_STATIC_LIBS=OFF -DGMX_X11=OFF
>
> ###
>
> -- Generating dependency file:
>
> /work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.NVCC-depend
> /software/CUDA/9.2.148/bin/nvcc -M -D__CUDACC__
> /work/GROMACS/gromacs-2018.3/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu -o
>
> /work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.NVCC-depend
> -ccbin /software/CUDA/9.2.148/bin/nvcc -m64 --std
> c++11 -Dlibgromacs_EXPORTS -DGMX_DOUBLE=0 -DHAVE_CONFIG_H
> -DUSE_STD_INTTYPES_H -Xcompiler
>
> ,\"-mavx512f\",\"-mfma\",\"-fPIC\",\"-O3\",\"-DNDEBUG\",\"-funroll-all-loops\",\"-fexcess-precision=fast\"
> -gencode arch=compute_60,code=sm_60 -gencode
> arch=compute_60,code=compute_60 -use_fast_math -gencode
> arch=compute_60,code=compute_60 -use_fast_math -D_FORCE_INLINES -DNVCC
> -I/software/CUDA/9.2.148/include
> -I/work/GROMACS/gromacs-2018.3/src/external/lmfit
>
> -I/work/GROMACS/gromacs-2018.3-build/src/contrib/fftw/fftwBuild-prefix/include
> -I/work/GROMACS/gromacs-2018.3-build/src
> -I/work/GROMACS/gromacs-2018.3/src/external/thread_mpi/include
> -I/work/GROMACS/gromacs-2018.3/src
> -I/software/hwloc/1.11.11-GCCcore-6.4.0/include
> -I/work/GROMACS/gromacs-2018.3/src/external/tng_io/include
> -I/work/GROMACS/gromacs-2018.3-build/tng/include*nvcc fatal   :
> 'avx512f': expected a number
> CMake Error at libgromacs_generated_nbnxn_cuda.cu.o.Release.cmake:219
> (message):
>   Error generating
>
>
> /work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/./libgromacs_generated_nbnxn_cuda.cu.o*
> --
> 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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[gmx-users] acpype

[Farial Tavakoli]

Dear GMX useres

I am trying to convert .OFF and .FRCMOD files obtained from AMBER parameter
database (Bryce Group: Computational Biophysics and Drug Design -
University of Manchester)
 to the format that
GROMACS is compatible with in .rtp files*. so referred to GROMACS tutorial
protein-ligand complex and downloaded acpype. installed it using its
readme.txt file but whenever i typed../acpype.py -i FFF.pdb   At folder
*acpype/test*   (/Downloads/acpype-master/acpype) or
(/Downloads/acpype-master/acpype/test) faced to this error:*


*bash: ../acpype.py: No such file or directory*

*while when I typed whereis acpype in terminal , the operating system says
:*


*acpype: /usr/local/bin/acpype*
* it means there is the executable file of acpype . so how come I type
../acpype.py -h or ../acpype -i FFF.pdb , the system says NO such file or
directory?*
*Is there anyone who ca help me?*
*I really would be appreciated it if one help me to solve this and can
convert the AMBER format files to GRMACS format files.*

*best regards*
*Farial*
-- 
Gromacs Users mailing list

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[gmx-users] acpype

[farial tavakoli]

Dear GMX useres
I am trying to convert .OFF and .FRCMOD files obtained from AMBER parameter 
database (Bryce Group: Computational Biophysics and Drug Design - University of 
Manchester) to the format that GROMACS is compatible with in .rtp files. so 
referred to GROMACS tutorial protein-ligand complex and downloaded acpype. 
installed it using its readme.txt file but whenever i typed    ../acpype.py -i 
FFF.pdb   At folder *acpype/test*   (/Downloads/acpype-master/acpype) or    
(/Downloads/acpype-master/acpype/test) faced to this error:
bash: ../acpype.py: No such file or directory

while when I typed whereis acpype in terminal , the operating system says 
:acpype: /usr/local/bin/acpype

 it means there is the executable file of acpype . so how come I type  
../acpype.py -h or ../acpype -i FFF.pdb , the system says NO such file or 
directory?Is there anyone who ca help me?I really would be appreciated it if 
one help me to solve this and can convert the AMBER format files to GRMACS 
format files.
best regardsFarial
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[gmx-users] nvcc fatal: 'avx512f': expected a number

[Ehsan Moravveji]

Dear GMX users,

I would like to share a difficulty installing GROMACS/2018.3 with you,
and kindly ask for your wisdom.

I use GCC/6.4.0 on a Linux cluster with CentOS 7.5 kernel and GPU
nodes equipped with 4 x P100 Nvidia devices.


Below is the cmake configuration that I use, followed by the error (in
boldface font) that I
receive. I am not sure if there is still an extra flag to set to resolve
this issue, or some other steps must be taken?

I appreciate your input.

-- 
Kind regards,
Ehsan Moravveji

###
cmake "${cwd}/${dir_src}" \
  -DGMX_SIMD='AVX_512' \
  -DBLAS_mkl_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \
  -DLAPACK_mkl_lapack_LIBRARY="DIR_MKL_LIB/libmkl_sequential.so" \
  -DBLAS_guide_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \
  -DCMAKE_C_COMPILER="${GMX_MPICC}" -DCMAKE_CXX_COMPILER="${GMX_MPICXX}" \
  -DMPI_C_COMPILER="${GMX_MPICC}" -DMPI_CXX_COMPILER="${GMX_MPICXX}" \
  -DCMAKE_MPI_C_COMPILER="${GMX_MPICC}"
-DCMAKE_MPI_CXX_COMPILER="${GMX_MPICXX}" \
  -DCMAKE_INSTALL_PREFIX="${dir_install}" \
  -DCMAKE_PREFIX_PATH="${DIR_MKL_LIB}" \
  -DCMAKE_VERBOSE_MAKEFILE=ON \
  -DGMX_MPI=ON \
  -DGMX_GPU=ON \
  -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF -DEXTRA_CXX_FLAGS="-std=c++11" \
  -DGMX_USE_NVML=ON -DGMX_BUILD_OWN_FFTW=ON \
  -DHWLOC_INCLUDE_DIRS="${EBROOTHWLOC}/include"
-DHWLOC_LIBRARIES="${EBROOTHWLOC}/lib/libhwloc.so" \
  -DCUDA_HOST_COMPILER="${PATH_NVCC}"
-DNVML_INCLUDE_DIR="${EBROOTCUDA}/include" \
  -DNVML_LIBRARY="${EBROOTCUDA}/lib64/stubs/libnvidia-ml.so" \
  -DCUDA_TOOLKIT_ROOT_DIR="${EBROOTCUDA}"
-DCUDA_SDK_ROOT_DIR="${EBROOTCUDA}" \
  -DCUDA_PROPAGATE_HOST_FLAGS=ON -DCUDA_VERBOSE_BUILD=ON \
  -DGMX_CUDA_TARGET_SM="${SM_VER}" -DGMX_CUDA_TARGET_COMPUTE="${SM_VER}" \
  -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF \
  -DCUDA_CUDART_LIBRARY="${EBROOTCUDA}/lib64/libcudart.so"
-DCUDA_CUDA_LIBRARY="${EBROOTCUDA}/lib64/libcuda.so" \

-DCUDA_NVCC_FLAGS="-gencode;arch=compute_${SM_VER},code=compute_${SM_VER};-use_fast_math;-D_FORCE_INLINES"
\
  -DGMX_PREFER_STATIC_LIBS=OFF -DGMX_X11=OFF

###

-- Generating dependency file:
/work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.NVCC-depend
/software/CUDA/9.2.148/bin/nvcc -M -D__CUDACC__
/work/GROMACS/gromacs-2018.3/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu -o
/work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.NVCC-depend
-ccbin /software/CUDA/9.2.148/bin/nvcc -m64 --std
c++11 -Dlibgromacs_EXPORTS -DGMX_DOUBLE=0 -DHAVE_CONFIG_H
-DUSE_STD_INTTYPES_H -Xcompiler
,\"-mavx512f\",\"-mfma\",\"-fPIC\",\"-O3\",\"-DNDEBUG\",\"-funroll-all-loops\",\"-fexcess-precision=fast\"
-gencode arch=compute_60,code=sm_60 -gencode
arch=compute_60,code=compute_60 -use_fast_math -gencode
arch=compute_60,code=compute_60 -use_fast_math -D_FORCE_INLINES -DNVCC
-I/software/CUDA/9.2.148/include
-I/work/GROMACS/gromacs-2018.3/src/external/lmfit
-I/work/GROMACS/gromacs-2018.3-build/src/contrib/fftw/fftwBuild-prefix/include
-I/work/GROMACS/gromacs-2018.3-build/src
-I/work/GROMACS/gromacs-2018.3/src/external/thread_mpi/include
-I/work/GROMACS/gromacs-2018.3/src
-I/software/hwloc/1.11.11-GCCcore-6.4.0/include
-I/work/GROMACS/gromacs-2018.3/src/external/tng_io/include
-I/work/GROMACS/gromacs-2018.3-build/tng/include*nvcc fatal   :
'avx512f': expected a number
CMake Error at libgromacs_generated_nbnxn_cuda.cu.o.Release.cmake:219
(message):
  Error generating

/work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/./libgromacs_generated_nbnxn_cuda.cu.o*
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Re: [gmx-users] Location of latest version of Acpype

[Alan]

Please, see here https://github.com/alanwilter/acpype

And many thanks for using ACPYPE!

Alan

On Tue, 23 Oct 2018 at 21:02, Matthew Fisher 
wrote:

> Dear all,
>
>
> I'm currently trying to locate the latest version of acpype and have been
> unable to find a working link to the script/installer. Could anyone please
> point me in the right direction?
>
>
> Thanks,
>
> Matthew Fisher
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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> send a mail to gmx-users-requ...@gromacs.org.
>


-- 
*I**​ have just cycled* from Land's End to John O'Groats​​​ (the
whole Britain!)
for a charity, would you consider​ ​supporting my​ cause?
http://uk.virginmoneygiving.com/AlanSilva
--
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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Re: [gmx-users] missing atoms in residues

[Bratin Kumar Das]

Use whatif server to complete ur structure

On Wed, Oct 24, 2018, 11:57 AM Rahma Dahmani 
wrote:

> Hi everyone,
> I have one question: Is it possible to add missing atoms in residues using
> gromacs ? ( PS. i already tried pdb2gmx but it didn't work out)
> missing atoms are :
> GLU A  117CB   CG   CD   OE1  OE2
> PRO A  158CB   CG   CD
>
> Thank you!
> --
>
>
>
>
>
>
> *Rahma Dahmani Doctorante en CHIMIE Unité de Recherche: Physico-Chimie des
> Matériaux à l'état condensé, Laboratoire de Chimie Théorique et
> Spectroscopie MoléculaireUniversité de Tunis El Manar, Faculté des Sciences
> de Tunis Campus Universitaire Farhat Hached - BP n ° 94 - Rommana 1068,
> Tunisie Tél: (+216) 28151042*
> --
> 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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Re: [gmx-users] parameters for plotting 2D density map with gmx densmap and xpm2ps

[Wenjuan Jiang]

Hello  Stéphane,

I happened to use densmap and xpm these days for my ion channel.

Here is an example that you can play with for your system.

gmx densmap -f md.xtc -s md.tpr -n index.ndx -aver z -bin 0.05 -dmin 0
-dmax 20 -unit nm-2 -o md.xpm
( later choose the group you are interested in)

-aver z means we want to get top view, that is going to show your dense map
in xy plane.
-bin width, you can play with it to get best view.  more options, you can
check with densmap -h

gmx xmp2ps -f md.xpm -o md.eps -rainbow blue

eps file can be opened either by eps viewer or photoshop.

Thanks,
Best
Wenjuan


On Tue, Oct 23, 2018 at 7:49 AM ABEL Stephane  wrote:

> Dear all,
>
> I would like to obtain a 2D density map plot as for instance Fig. 4 in the
> following paper (DOI 10.1007/s00232-014-9690-8) for a membrane protein
> inserted in a surfactant micelle with gmx densmap and xpm2ps .  I have few
> questions
>
> - Have any of you ever done this type of plot? If yes, how?
> - What parameters for densmap and/or xpm2ps did you use?
> - How did you combine the protein and surfactant xpm files into a single
> one to obtain the same plot as Fig. 4
>
> Thanks in advance for your help
>
> Stéphane
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>


-- 
Best regards

Wenjuan Jiang
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[gmx-users] missing atoms in residues

[Rahma Dahmani]

Hi everyone,
I have one question: Is it possible to add missing atoms in residues using
gromacs ? ( PS. i already tried pdb2gmx but it didn't work out)
missing atoms are :
GLU A  117CB   CG   CD   OE1  OE2
PRO A  158CB   CG   CD

Thank you!
-- 






*Rahma Dahmani Doctorante en CHIMIE Unité de Recherche: Physico-Chimie des
Matériaux à l'état condensé, Laboratoire de Chimie Théorique et
Spectroscopie MoléculaireUniversité de Tunis El Manar, Faculté des Sciences
de Tunis Campus Universitaire Farhat Hached - BP n ° 94 - Rommana 1068,
Tunisie Tél: (+216) 28151042*
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