[gmx-users] difference in rvdw , rlist parameters in em and nvt steps

[Mahboobe Sadr]

Dear all users,

In mdp files in ligand tutorial,  rvdw,rlist.are equal to 1 in em step,.
And are equal to 1.4 in nvt,npt and production md

When we can set different interaction parameters for different step?

Best regards
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Re: [gmx-users] Weird configuration when pulling rate is small

[Erik Marklund]

Dear Ming,

Sounds like a visualisation problem. Does it persist if you e.g. translate the 
system with trjconv?

Kind regards,
Erik

> On 11 Feb 2016, at 00:44, Ming Tang  wrote:
> 
> Dear list,
> 
> I am pulling a triple helix using umbrella distance. When the pulling rate is 
> 0.0004 nm/ps, the configuration is normal. However, when I decrease the 
> pulling rate to 0.0002 nm/ps or lower, the configuration is messy (some atoms 
> flow away from the triple helix), but the simulations run well and both the 
> force_strain curve and the history of number of h_bonds  look normal. Could 
> anybody tell me why is that low pulling rates cause this problem?
> 
> Thanks in advance,
> Ming
> 
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Re: [gmx-users] difference in rvdw , rlist parameters in em and nvt steps

[Mark Abraham]

Hi,

On Thu, Feb 11, 2016 at 9:46 AM Mahboobe Sadr 
wrote:

> Dear all users,
>
> In mdp files in ligand tutorial,  rvdw,rlist.are equal to 1 in em step,.
> And are equal to 1.4 in nvt,npt and production md
>
> When we can set different interaction parameters for different step?
>

You should choose such parameters based on those used for the
parametrization of the force field, and/or subsequent reports of successful
applications of them, particularly by the original authors.

As you no doubt learned from the tutorial, EM is commonly used for relaxing
inconsistencies in the starting geometry so that equilibration can proceed
stably. Experience shows that short-range settings that are ultra faithful
to the force field do not materially improve the success of equilibration -
anything normally does the job fine.

Mark

Best regards
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Re: [gmx-users] Weird configuration when pulling rate is small

[Ming Tang]

Dear Erik,

Thanks for your advice. I think you are right. However, when using -pbc whole, 
every chain is intact but the three chains separate in some frames; when using 
-pbc nojump, the collagen molecule is not intact (there is a small part stay in 
the other box ) either. If I fix one end, and use -pbc whole, the problem is 
fixed.
Thanks and regards,
Ming
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Re: [gmx-users] difference in rvdw , rlist parameters in em and nvt steps

[M S]

I thought  the tutorial set the em parameters lower than nvt parameters based 
on a specific reason. So there is no specific reason in tutorial?

Best regards

Sent using Boxer

On Feb 11, 2016 12:22 PM, Mark Abraham  wrote:

Hi,

On Thu, Feb 11, 2016 at 9:46 AM Mahboobe Sadr 
wrote:

> Dear all users,
>
> In mdp files in ligand tutorial,  rvdw,rlist.are equal to 1 in em step,.
> And are equal to 1.4 in nvt,npt and production md
>
> When we can set different interaction parameters for different step?
>

You should choose such parameters based on those used for the
parametrization of the force field, and/or subsequent reports of successful
applications of them, particularly by the original authors.

As you no doubt learned from the tutorial, EM is commonly used for relaxing
inconsistencies in the starting geometry so that equilibration can proceed
stably. Experience shows that short-range settings that are ultra faithful
to the force field do not materially improve the success of equilibration -
anything normally does the job fine.

Mark

Best regards
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[gmx-users] View Trajectory - Water Expansion

[Natalie Stephenson]

Hi all,

I'm experiencing a problem with my trajectory waters. Really early on in the 
simulation the waters begin expanding out of the box. There are no system 
errors that I am aware of and the simulation runs fine.

Is this something that can be fixed with trjconv? Or is it something more 
worrying with regards to the simulation run? I'm currently using trjconv with 
-pbc nojump, resulting in the protein looking fine, but the waters are another 
matter.

I've tried searching for this issue but couldn't find other mention of it.

Thanks for any help that you can offer.

Natalie

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Re: [gmx-users] complex topology file

[Justin Lemkul]

Please keep the discussion on the mailing list.

On 2/10/16 10:31 PM, Sana Saeed wrote:

My question is, even if i use Acpype , and follow the steps of making complex
files as in tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
 can
I use these files for MD of binding free energy calculation or I have to make
them in different way.



Assuming you're using the protocol using an AMBER force field instead of GROMOS, 
then probably the Acpype output is OK.  Many people use it, but I haven't so I 
can't comment on it.  But if you're going to be parametrizing new things, you 
should have a good understanding of the parent force field, what its assumptions 
and parametrization methods are, and how parameters are validated.  Then you can 
assess how good of a ligand topology you have.


-Justin


Sana Saeed Khan,
Teaching-Research Assistant
Chemoinformatics Lab
Graduate Student, MS bioinfo
Department of Bioinformatics
Soongsil University, Seoul, South Korea.


On Thursday, February 11, 2016 10:42 AM, Justin Lemkul  wrote:




On 2/10/16 8:34 PM, Sana Saeed wrote:
 > please someone help me. i want to find out absolute binding free energy of
 > protein ligand complex. fisrt i performed docking and selected best poses and
 > then i made topology file of ligand with PRODRGserver. and then included itp
 > file of ligand in Protein topology file (from pdb2gmx) , also made
 > complex.gro as in tutorial
 >
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
 > . can i use these complex files for MD for absolute binding free energy? in
 > some tutorials the topology file of complex is quite differently organised.
 > please guide me, i am following decoupling and coupling steps from
 >
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme

 >

I already replied:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-February/103524.html

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu  |
(410) 706-7441
http://mackerell.umaryland.edu/~jalemkul


==




--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] difference in rvdw , rlist parameters in em and nvt steps

[M S]

It was very helpful... thanks a lot. 

Sent using Boxer

On Feb 11, 2016 2:20 PM, Justin Lemkul  wrote:



On 2/11/16 5:28 AM, M S wrote:
> I thought  the tutorial set the em parameters lower than nvt parameters based 
> on a specific reason. So there is no specific reason in tutorial?
>

No.  Generally I aim to keep them the same throughout, for consistency.  In 
this 
case, it's just an oversight, but one that produces no practical detriment.  As 
Mark says, for the purposes of EM, it works.  And I have, in fact, tested that 
you get plausible results during EM even with different cutoffs.  Not generally 
a wise practice to be toying with such things, but for EM there is no real 
problem.  During dynamics is a whole other story.

-Justin

> Best regards
>
> Sent using Boxer
>
> On Feb 11, 2016 12:22 PM, Mark Abraham  wrote:
>
> Hi,
>
> On Thu, Feb 11, 2016 at 9:46 AM Mahboobe Sadr 
> wrote:
>
>> Dear all users,
>>
>> In mdp files in ligand tutorial,  rvdw,rlist.are equal to 1 in em step,.
>> And are equal to 1.4 in nvt,npt and production md
>>
>> When we can set different interaction parameters for different step?
>>
>
> You should choose such parameters based on those used for the
> parametrization of the force field, and/or subsequent reports of successful
> applications of them, particularly by the original authors.
>
> As you no doubt learned from the tutorial, EM is commonly used for relaxing
> inconsistencies in the starting geometry so that equilibration can proceed
> stably. Experience shows that short-range settings that are ultra faithful
> to the force field do not materially improve the success of equilibration -
> anything normally does the job fine.
>
> Mark
>
> Best regards
>> --
>> 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.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] difference in rvdw , rlist parameters in em and nvt steps

[Mark Abraham]

Hi,

That's up to the author of the tutorial. Smaller list sizes are faster to
run, and if the purpose of the EM is to ensure that equilibration succeeds,
then anything that works, works.

Mark

On Thu, Feb 11, 2016 at 11:28 AM M S  wrote:

> I thought  the tutorial set the em parameters lower than nvt parameters
> based on a specific reason. So there is no specific reason in tutorial?
>
> Best regards
>
> Sent using Boxer
>
> On Feb 11, 2016 12:22 PM, Mark Abraham  wrote:
>
> Hi,
>
> On Thu, Feb 11, 2016 at 9:46 AM Mahboobe Sadr  >
> wrote:
>
> > Dear all users,
> >
> > In mdp files in ligand tutorial,  rvdw,rlist.are equal to 1 in em step,.
> > And are equal to 1.4 in nvt,npt and production md
> >
> > When we can set different interaction parameters for different step?
> >
>
> You should choose such parameters based on those used for the
> parametrization of the force field, and/or subsequent reports of successful
> applications of them, particularly by the original authors.
>
> As you no doubt learned from the tutorial, EM is commonly used for relaxing
> inconsistencies in the starting geometry so that equilibration can proceed
> stably. Experience shows that short-range settings that are ultra faithful
> to the force field do not materially improve the success of equilibration -
> anything normally does the job fine.
>
> Mark
>
> Best regards
> > --
> > 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
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[gmx-users] Choosing Parameter values of PTMs

[David Newman]

Hi all,

I'm starting a MD project using gromacs and we're looking to expand on the 
previous work in the lab modelling our receptors of interest by looking at the 
effects of gylcosylation. Is there a current best standard for parameters for 
modelling glycans?

Thanks,
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Re: [gmx-users] difference in rvdw , rlist parameters in em and nvt steps

[M S]

Thanks for replying so fast.

Sent using Boxer

On Feb 11, 2016 2:05 PM, Mark Abraham  wrote:

Hi,

That's up to the author of the tutorial. Smaller list sizes are faster to
run, and if the purpose of the EM is to ensure that equilibration succeeds,
then anything that works, works.

Mark

On Thu, Feb 11, 2016 at 11:28 AM M S  wrote:

> I thought  the tutorial set the em parameters lower than nvt parameters
> based on a specific reason. So there is no specific reason in tutorial?
>
> Best regards
>
> Sent using Boxer
>
> On Feb 11, 2016 12:22 PM, Mark Abraham  wrote:
>
> Hi,
>
> On Thu, Feb 11, 2016 at 9:46 AM Mahboobe Sadr  >
> wrote:
>
> > Dear all users,
> >
> > In mdp files in ligand tutorial,  rvdw,rlist.are equal to 1 in em step,.
> > And are equal to 1.4 in nvt,npt and production md
> >
> > When we can set different interaction parameters for different step?
> >
>
> You should choose such parameters based on those used for the
> parametrization of the force field, and/or subsequent reports of successful
> applications of them, particularly by the original authors.
>
> As you no doubt learned from the tutorial, EM is commonly used for relaxing
> inconsistencies in the starting geometry so that equilibration can proceed
> stably. Experience shows that short-range settings that are ultra faithful
> to the force field do not materially improve the success of equilibration -
> anything normally does the job fine.
>
> Mark
>
> Best regards
> > --
> > 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
>
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> posting!
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Re: [gmx-users] difference in rvdw , rlist parameters in em and nvt steps

[Justin Lemkul]

On 2/11/16 5:28 AM, M S wrote:

I thought  the tutorial set the em parameters lower than nvt parameters based 
on a specific reason. So there is no specific reason in tutorial?



No.  Generally I aim to keep them the same throughout, for consistency.  In this 
case, it's just an oversight, but one that produces no practical detriment.  As 
Mark says, for the purposes of EM, it works.  And I have, in fact, tested that 
you get plausible results during EM even with different cutoffs.  Not generally 
a wise practice to be toying with such things, but for EM there is no real 
problem.  During dynamics is a whole other story.


-Justin


Best regards

Sent using Boxer

On Feb 11, 2016 12:22 PM, Mark Abraham  wrote:

Hi,

On Thu, Feb 11, 2016 at 9:46 AM Mahboobe Sadr 
wrote:


Dear all users,

In mdp files in ligand tutorial,  rvdw,rlist.are equal to 1 in em step,.
And are equal to 1.4 in nvt,npt and production md

When we can set different interaction parameters for different step?



You should choose such parameters based on those used for the
parametrization of the force field, and/or subsequent reports of successful
applications of them, particularly by the original authors.

As you no doubt learned from the tutorial, EM is commonly used for relaxing
inconsistencies in the starting geometry so that equilibration can proceed
stably. Experience shows that short-range settings that are ultra faithful
to the force field do not materially improve the success of equilibration -
anything normally does the job fine.

Mark

Best regards

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send a mail to gmx-users-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] View Trajectory - Water Expansion

[Justin Lemkul]

On 2/11/16 7:13 AM, Natalie Stephenson wrote:

Hi all,

I'm experiencing a problem with my trajectory waters. Really early on in the 
simulation the waters begin expanding out of the box. There are no system 
errors that I am aware of and the simulation runs fine.

Is this something that can be fixed with trjconv? Or is it something more 
worrying with regards to the simulation run? I'm currently using trjconv with 
-pbc nojump, resulting in the protein looking fine, but the waters are another 
matter.



Waters are diffusing "out" of the box (which can't actually happen) as a result 
of using -pbc nojump; that's it's function.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Choosing Parameter values of PTMs

[bipin singh]

You can have a look at few related work:

http://selene.princeton.edu/FFPTM/
http://vienna-ptm.univie.ac.at/
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003154


--
Thanks and Regards,
Bipin Singh

On Thu, Feb 11, 2016 at 6:29 PM, David Newman <
david.newma...@postgrad.manchester.ac.uk> wrote:

> Hi all,
>
> I'm starting a MD project using gromacs and we're looking to expand on the
> previous work in the lab modelling our receptors of interest by looking at
> the effects of gylcosylation. Is there a current best standard for
> parameters for modelling glycans?
>
> Thanks,
> --
> 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
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Choosing Parameter values of PTMs

[Krzysztof Kuczera]

Take a look at the CHARMM-GUI input generator - that allows you to set 
up simulations for glycans and various glycosylated systems


Krzysztof Kuczera

On 2/11/16 6:59 AM, David Newman wrote:

Hi all,

I'm starting a MD project using gromacs and we're looking to expand on the 
previous work in the lab modelling our receptors of interest by looking at the 
effects of gylcosylation. Is there a current best standard for parameters for 
modelling glycans?

Thanks,



--
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
1251 Wescoe Hall Drive, 5090 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html

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Re: [gmx-users] add parameter

[Justin Lemkul]

On 2/11/16 12:03 PM, Malihe Hasanzadeh wrote:

Hi
I have three water molecules and one new residue that I want to add their
parameters to force field Amber99sb. One of water molecules has only one
hydrogen, and since I want to prevent from replacing with SOL in solvation
step, So I define them as new residue in .rtp file:

[ INN ]
  [ atoms ]
H1H   0.384620 1
 OO  -0.671930 2
H2H   0.384620 3


[ INT ]
  [ atoms ]
H1H   0.286310 1
 OO  -0.341910 2
H2H   0.286310 3


[ INB ]
  [ atoms ]
H1H   0.477860 1
 OO  -1.092580 2
Also define them in .dat file as Protein  and in .hdb file as below:



Defining these residues as protein is not necessary.


INN2
17H1O
17H2O
INT2
17H1O
17H2O
INB1
17H1O

But when I start MD simulation(gromacs 5.0.4) in step of mdrun ...em,
gives segmentation fault! when I remove their parameters in .hdb file, it
is done but without any hydrogen for them, just three oxygen atoms in
em.gro!



This is because you would have had to invoke -missing with pdb2gmx and yield 
something totally useless.


Immediate seg faults are indicative of complete instability.  Note that none of 
your .rtp entries have [bonds] defined, so you probably just have particles very 
close to one another (e.g. as they would be in a real molecule) but no covalent 
attachment, so they likely just fly apart.



Also I have another problem with that new residue, this residue is like a
Lys but has two carbonyl groups binded to extra carbon instead of amino
group in Lys. So I used Lys parameters for that and add some bonds and
atoms to it:

[ NEW ] ;
  [ atoms ]
 N   N
 H   H
CA   CT
HAH1
CB   CT
   HB1   HC
   HB2   HC
CG  CT
   HG1  H
   HG2  H
CD  CT
   HD1  HC
   HD2  HC
CE  CT
   HE1  HP
   HE2  HP
NZ  N
HZ  H
CX  C
   OQ1 O
   OQ2 O
 C  C
 O  O
  [ bonds ]
  N H
  NCA
 CAHA
 CACB
 CA C
 CB   HB1
 CB   HB2
 CBCG
 CG   HG1
 CG   HG2
 CGCD
 CD   HD1
 CD   HD2
 CDCE
 CE   HE1
 CE   HE2
 CENZ
 NZHZ
 NZCX
  C O
 CX   OQ1
 CX   OQ2
  [ impropers ]
 -CCA N H
 CA+N C O
when I added only atoms parameters in .rtp file, finally in em.gro file
there wasn't any bond between atoms of new residue and when I added bond


As you should expect.  See above.  [bonds] is a mandatory directive (which is 
also stated clearly in the manual).



parameters also, in grompp gives 10 error about "default angel and
dihedral"! I find the number of angels in .top file and added them to
ffbonded.itp, but anything have no change.


You're adding moieties that don't exist in the force field, unless you have 
parameters from some external source (e.g. something published or otherwise 
available in a force field repository).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Gromacs Users mailing list

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mail to gmx-users-requ...@gromacs.org.

[gmx-users] add parameter

[Malihe Hasanzadeh]

Hi
I have three water molecules and one new residue that I want to add their
parameters to force field Amber99sb. One of water molecules has only one
hydrogen, and since I want to prevent from replacing with SOL in solvation
step, So I define them as new residue in .rtp file:

[ INN ]
 [ atoms ]
   H1H   0.384620 1
OO  -0.671930 2
   H2H   0.384620 3


[ INT ]
 [ atoms ]
   H1H   0.286310 1
OO  -0.341910 2
   H2H   0.286310 3


[ INB ]
 [ atoms ]
   H1H   0.477860 1
OO  -1.092580 2
Also define them in .dat file as Protein  and in .hdb file as below:

INN2
17H1O
17H2O
INT2
17H1O
17H2O
INB1
17H1O

But when I start MD simulation(gromacs 5.0.4) in step of mdrun ...em,
gives segmentation fault! when I remove their parameters in .hdb file, it
is done but without any hydrogen for them, just three oxygen atoms in
em.gro!

Also I have another problem with that new residue, this residue is like a
Lys but has two carbonyl groups binded to extra carbon instead of amino
group in Lys. So I used Lys parameters for that and add some bonds and
atoms to it:

[ NEW ] ;
 [ atoms ]
N   N
H   H
   CA   CT
   HAH1
   CB   CT
  HB1   HC
  HB2   HC
   CG  CT
  HG1  H
  HG2  H
   CD  CT
  HD1  HC
  HD2  HC
   CE  CT
  HE1  HP
  HE2  HP
   NZ  N
   HZ  H
   CX  C
  OQ1 O
  OQ2 O
C  C
O  O
 [ bonds ]
 N H
 NCA
CAHA
CACB
CA C
CB   HB1
CB   HB2
CBCG
CG   HG1
CG   HG2
CGCD
CD   HD1
CD   HD2
CDCE
CE   HE1
CE   HE2
CENZ
NZHZ
NZCX
 C O
CX   OQ1
CX   OQ2
 [ impropers ]
-CCA N H
CA+N C O
when I added only atoms parameters in .rtp file, finally in em.gro file
there wasn't any bond between atoms of new residue and when I added bond
parameters also, in grompp gives 10 error about "default angel and
dihedral"! I find the number of angels in .top file and added them to
ffbonded.itp, but anything have no change.
please help me. what is my mistake about these two insistent problems?
Thanks
Malihe
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Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

[Irina Kosheleva]

No, I'm not sure. As a matter of fact I was not able to  find source of 
libxml2-devel  (+xz-devel, +zlib-devel)  (tar.gz)  for this arch to install it 
as a user. You might be right on this comment.
Thank you.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Smith, 
Micholas D.
Sent: Thursday, February 11, 2016 11:33 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

Quick clarifying question, are you sure you have the development version of the 
libxml2 package (the source with the headers and everything)?

Also this might be a good time to complain to your sys-admin to install the 
libxml2-dev library, as it is used in a lot of other programs too, and you 
would just be saving everyone a headache.


===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Irina 
Kosheleva 
Sent: Thursday, February 11, 2016 12:08 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] gromacs-5.1.1 installation error:  libxml2 problem

Dear gmx-users.
I would like to install gromacs-5.1.1 on a cluster where I have only user 
privileges. The machine has arch linux-rhel_6-ppc64.
I would like to install it with unittest support thus I need libxml2.a compiled 
library.
The cluster does not have this library installed so I have downloaded 
libxml2-2.9.2 and compiled it with zlib support:
 ./configure --prefix=/home/ikosh/programs/autotools-bin 
--with-python-install-dir=/home/ikosh/programs/autotools-bin 
--with-zlib=/soft/libraries/alcf/current/xl/ZLIB

Now, I would like to use this static libxml2.a library to compile gromacs-5.1.1:
cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r 
-DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX 
-DFFTWF_INCLUDE_DIR=/soft/libraries/alcf/current/xl/FFTW3/include 
-DFFTWF_LIBRARY=/soft/libraries/alcf/current/xl/FFTW3/lib/libfftw3f.a 
-DLIBXML2_INCLUDE_DIR=/gpfs/vesta-home/ikosh/programs/autotools-bin/include  
-DLIBXML2_LIBRARIES=/gpfs/vesta-home/ikosh/programs/autotools-bin/lib/libxml2.a 
-DZLIB_INCLUDE_DIR=/soft/libraries/soft/libraries/alcf/current/xl/ZLIB/include 
-DZLIB=/soft/libraries/alcf/current/xl/ZLIB/lib/libz.a
-DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF -DGMX_PREFER_STATIC_LIBS=ON  
-DCMAKE_C_FLAGS="-O3 -qsmp=omp -qarch=qp -qtune=qp" 
-DCMAKE_INSTALL_PREFIX=/gpfs/vesta-home/ikosh/gromacs-5.1.1/install

--output  just the error:
-- Looking for xmlTextWriterEndAttribute in 
/home/ikosh/programs/autotools-bin/lib/libxml2.a
-- Looking for xmlTextWriterEndAttribute in 
/home/ikosh/programs/autotools-bin/lib/libxml2.a - not found
CMake Warning at CMakeLists.txt:543 (message):
  libxml2 not found.  Will build GROMACS without unit-tests.  This is not
  recommended, because the unit-tests help to verify that GROMACS functions
  correctly.  Most likely you are missing the libxml2-dev(el) package.  After
  you installed it, set GMX_BUILD_UNITTESTS=ON.

Looking at the CMakeError.log in CMakeFiles:
/soft/buildtools/cmake/3.3.0/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_09bc5.dir/link.txt --verbose=1
/soft/compilers/wrappers/xl/mpixlc_r  -Wl,-relax -O3 -qsmp=omp -qarch=qp 
-qtune=qp -qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-03
0 -qlanglvl=extc99 -qarch=auto -qtune=auto  
-DCHECK_FUNCTION_EXISTS=xmlTextWriterEndAttribute
CMakeFiles/cmTC_09bc5.dir/CheckFunctionExist
s.c.o  -o cmTC_09bc5  /home/ikosh/programs/autotools-bin/lib/libxml2.a
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileOpenW':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1275: undefined reference to 
`gzopen64'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1246: undefined reference to 
`gzdopen'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`__xmlParserInputBufferCreateFilename':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:2670: undefined reference to 
`gzdirect'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlFreeZMemBuff':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1556: undefined reference to 
`deflateEnd'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileOpen_real':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1167: undefined reference to 
`gzdopen'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1198: undefined reference to 
`gzopen64'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileClose':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1331: undefined reference to 
`gzclose'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileWrite':

Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

[Irina Kosheleva]

Hi Mark,
Exactly what location I can find them to include, do you know?
Irina.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: Thursday, February 11, 2016 11:47 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

Hi,

IIRC ALCF does make available libxml2 with headers for bgq on Vesta, so I'm
sure the have/will on Mira too! Ask them.

Mark

On Thu, 11 Feb 2016 18:33 Smith, Micholas D.  wrote:

> Quick clarifying question, are you sure you have the development version
> of the libxml2 package (the source with the headers and everything)?
>
> Also this might be a good time to complain to your sys-admin to install
> the libxml2-dev library, as it is used in a lot of other programs too, and
> you would just be saving everyone a headache.
>
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Irina
> Kosheleva 
> Sent: Thursday, February 11, 2016 12:08 PM
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] gromacs-5.1.1 installation error:  libxml2 problem
>
> Dear gmx-users.
> I would like to install gromacs-5.1.1 on a cluster where I have only user
> privileges. The machine has arch linux-rhel_6-ppc64.
> I would like to install it with unittest support thus I need libxml2.a
> compiled library.
> The cluster does not have this library installed so I have downloaded
> libxml2-2.9.2 and compiled it with zlib support:
>  ./configure --prefix=/home/ikosh/programs/autotools-bin
> --with-python-install-dir=/home/ikosh/programs/autotools-bin
> --with-zlib=/soft/libraries/alcf/current/xl/ZLIB
>
> Now, I would like to use this static libxml2.a library to compile
> gromacs-5.1.1:
> cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r
> -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX
> -DFFTWF_INCLUDE_DIR=/soft/libraries/alcf/current/xl/FFTW3/include
> -DFFTWF_LIBRARY=/soft/libraries/alcf/current/xl/FFTW3/lib/libfftw3f.a
> -DLIBXML2_INCLUDE_DIR=/gpfs/vesta-home/ikosh/programs/autotools-bin/include
> -DLIBXML2_LIBRARIES=/gpfs/vesta-home/ikosh/programs/autotools-bin/lib/libxml2.a
> -DZLIB_INCLUDE_DIR=/soft/libraries/soft/libraries/alcf/current/xl/ZLIB/include
> -DZLIB=/soft/libraries/alcf/current/xl/ZLIB/lib/libz.a
> -DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF -DGMX_PREFER_STATIC_LIBS=ON
> -DCMAKE_C_FLAGS="-O3 -qsmp=omp -qarch=qp -qtune=qp"
> -DCMAKE_INSTALL_PREFIX=/gpfs/vesta-home/ikosh/gromacs-5.1.1/install
>
> --output  just the error:
> -- Looking for xmlTextWriterEndAttribute in
> /home/ikosh/programs/autotools-bin/lib/libxml2.a
> -- Looking for xmlTextWriterEndAttribute in
> /home/ikosh/programs/autotools-bin/lib/libxml2.a - not found
> CMake Warning at CMakeLists.txt:543 (message):
>   libxml2 not found.  Will build GROMACS without unit-tests.  This is not
>   recommended, because the unit-tests help to verify that GROMACS functions
>   correctly.  Most likely you are missing the libxml2-dev(el) package.
> After
>   you installed it, set GMX_BUILD_UNITTESTS=ON.
>
> Looking at the CMakeError.log in CMakeFiles:
> /soft/buildtools/cmake/3.3.0/bin/cmake -E cmake_link_script
> CMakeFiles/cmTC_09bc5.dir/link.txt --verbose=1
> /soft/compilers/wrappers/xl/mpixlc_r  -Wl,-relax -O3 -qsmp=omp -qarch=qp
> -qtune=qp -qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-03
> 0 -qlanglvl=extc99 -qarch=auto -qtune=auto
> -DCHECK_FUNCTION_EXISTS=xmlTextWriterEndAttribute
> CMakeFiles/cmTC_09bc5.dir/CheckFunctionExist
> s.c.o  -o cmTC_09bc5  /home/ikosh/programs/autotools-bin/lib/libxml2.a
> /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> `xmlGzfileOpenW':
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1275: undefined reference to
> `gzopen64'
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1246: undefined reference to
> `gzdopen'
> /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> `__xmlParserInputBufferCreateFilename':
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:2670: undefined reference to
> `gzdirect'
> /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> `xmlFreeZMemBuff':
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1556: undefined reference to
> `deflateEnd'
> /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> `xmlGzfileOpen_real':
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1167: undefined reference to
> `gzdopen'
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1198: undefined reference to
> `gzopen64'
> /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> 

Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

[Mark Abraham]

Hi,

I don't remember, but there are people paid to remember ;-)

Mark

On Thu, 11 Feb 2016 18:53 Irina Kosheleva 
wrote:

> Hi Mark,
> Exactly what location I can find them to include, do you know?
> Irina.
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
> Abraham
> Sent: Thursday, February 11, 2016 11:47 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem
>
> Hi,
>
> IIRC ALCF does make available libxml2 with headers for bgq on Vesta, so I'm
> sure the have/will on Mira too! Ask them.
>
> Mark
>
> On Thu, 11 Feb 2016 18:33 Smith, Micholas D.  wrote:
>
> > Quick clarifying question, are you sure you have the development version
> > of the libxml2 package (the source with the headers and everything)?
> >
> > Also this might be a good time to complain to your sys-admin to install
> > the libxml2-dev library, as it is used in a lot of other programs too,
> and
> > you would just be saving everyone a headache.
> >
> >
> > ===
> > Micholas Dean Smith, PhD.
> > Post-doctoral Research Associate
> > University of Tennessee/Oak Ridge National Laboratory
> > Center for Molecular Biophysics
> >
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Irina
> > Kosheleva 
> > Sent: Thursday, February 11, 2016 12:08 PM
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] gromacs-5.1.1 installation error:  libxml2 problem
> >
> > Dear gmx-users.
> > I would like to install gromacs-5.1.1 on a cluster where I have only user
> > privileges. The machine has arch linux-rhel_6-ppc64.
> > I would like to install it with unittest support thus I need libxml2.a
> > compiled library.
> > The cluster does not have this library installed so I have downloaded
> > libxml2-2.9.2 and compiled it with zlib support:
> >  ./configure --prefix=/home/ikosh/programs/autotools-bin
> > --with-python-install-dir=/home/ikosh/programs/autotools-bin
> > --with-zlib=/soft/libraries/alcf/current/xl/ZLIB
> >
> > Now, I would like to use this static libxml2.a library to compile
> > gromacs-5.1.1:
> > cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r
> > -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX
> > -DFFTWF_INCLUDE_DIR=/soft/libraries/alcf/current/xl/FFTW3/include
> > -DFFTWF_LIBRARY=/soft/libraries/alcf/current/xl/FFTW3/lib/libfftw3f.a
> >
> -DLIBXML2_INCLUDE_DIR=/gpfs/vesta-home/ikosh/programs/autotools-bin/include
> >
> -DLIBXML2_LIBRARIES=/gpfs/vesta-home/ikosh/programs/autotools-bin/lib/libxml2.a
> >
> -DZLIB_INCLUDE_DIR=/soft/libraries/soft/libraries/alcf/current/xl/ZLIB/include
> > -DZLIB=/soft/libraries/alcf/current/xl/ZLIB/lib/libz.a
> > -DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF -DGMX_PREFER_STATIC_LIBS=ON
> > -DCMAKE_C_FLAGS="-O3 -qsmp=omp -qarch=qp -qtune=qp"
> > -DCMAKE_INSTALL_PREFIX=/gpfs/vesta-home/ikosh/gromacs-5.1.1/install
> >
> > --output  just the error:
> > -- Looking for xmlTextWriterEndAttribute in
> > /home/ikosh/programs/autotools-bin/lib/libxml2.a
> > -- Looking for xmlTextWriterEndAttribute in
> > /home/ikosh/programs/autotools-bin/lib/libxml2.a - not found
> > CMake Warning at CMakeLists.txt:543 (message):
> >   libxml2 not found.  Will build GROMACS without unit-tests.  This is not
> >   recommended, because the unit-tests help to verify that GROMACS
> functions
> >   correctly.  Most likely you are missing the libxml2-dev(el) package.
> > After
> >   you installed it, set GMX_BUILD_UNITTESTS=ON.
> >
> > Looking at the CMakeError.log in CMakeFiles:
> > /soft/buildtools/cmake/3.3.0/bin/cmake -E cmake_link_script
> > CMakeFiles/cmTC_09bc5.dir/link.txt --verbose=1
> > /soft/compilers/wrappers/xl/mpixlc_r  -Wl,-relax -O3 -qsmp=omp -qarch=qp
> > -qtune=qp -qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-03
> > 0 -qlanglvl=extc99 -qarch=auto -qtune=auto
> > -DCHECK_FUNCTION_EXISTS=xmlTextWriterEndAttribute
> > CMakeFiles/cmTC_09bc5.dir/CheckFunctionExist
> > s.c.o  -o cmTC_09bc5  /home/ikosh/programs/autotools-bin/lib/libxml2.a
> > /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> > `xmlGzfileOpenW':
> > /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1275: undefined reference to
> > `gzopen64'
> > /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1246: undefined reference to
> > `gzdopen'
> > /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> > `__xmlParserInputBufferCreateFilename':
> > /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:2670: undefined reference to
> > `gzdirect'
> > /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> > `xmlFreeZMemBuff':
> > /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1556: undefined reference to
> > 

Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

[Irina Kosheleva]

Thank you, good point.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: Thursday, February 11, 2016 11:58 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

Hi,

I don't remember, but there are people paid to remember ;-)

Mark

On Thu, 11 Feb 2016 18:53 Irina Kosheleva 
wrote:

> Hi Mark,
> Exactly what location I can find them to include, do you know?
> Irina.
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
> Abraham
> Sent: Thursday, February 11, 2016 11:47 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem
>
> Hi,
>
> IIRC ALCF does make available libxml2 with headers for bgq on Vesta, so I'm
> sure the have/will on Mira too! Ask them.
>
> Mark
>
> On Thu, 11 Feb 2016 18:33 Smith, Micholas D.  wrote:
>
> > Quick clarifying question, are you sure you have the development version
> > of the libxml2 package (the source with the headers and everything)?
> >
> > Also this might be a good time to complain to your sys-admin to install
> > the libxml2-dev library, as it is used in a lot of other programs too,
> and
> > you would just be saving everyone a headache.
> >
> >
> > ===
> > Micholas Dean Smith, PhD.
> > Post-doctoral Research Associate
> > University of Tennessee/Oak Ridge National Laboratory
> > Center for Molecular Biophysics
> >
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Irina
> > Kosheleva 
> > Sent: Thursday, February 11, 2016 12:08 PM
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] gromacs-5.1.1 installation error:  libxml2 problem
> >
> > Dear gmx-users.
> > I would like to install gromacs-5.1.1 on a cluster where I have only user
> > privileges. The machine has arch linux-rhel_6-ppc64.
> > I would like to install it with unittest support thus I need libxml2.a
> > compiled library.
> > The cluster does not have this library installed so I have downloaded
> > libxml2-2.9.2 and compiled it with zlib support:
> >  ./configure --prefix=/home/ikosh/programs/autotools-bin
> > --with-python-install-dir=/home/ikosh/programs/autotools-bin
> > --with-zlib=/soft/libraries/alcf/current/xl/ZLIB
> >
> > Now, I would like to use this static libxml2.a library to compile
> > gromacs-5.1.1:
> > cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r
> > -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX
> > -DFFTWF_INCLUDE_DIR=/soft/libraries/alcf/current/xl/FFTW3/include
> > -DFFTWF_LIBRARY=/soft/libraries/alcf/current/xl/FFTW3/lib/libfftw3f.a
> >
> -DLIBXML2_INCLUDE_DIR=/gpfs/vesta-home/ikosh/programs/autotools-bin/include
> >
> -DLIBXML2_LIBRARIES=/gpfs/vesta-home/ikosh/programs/autotools-bin/lib/libxml2.a
> >
> -DZLIB_INCLUDE_DIR=/soft/libraries/soft/libraries/alcf/current/xl/ZLIB/include
> > -DZLIB=/soft/libraries/alcf/current/xl/ZLIB/lib/libz.a
> > -DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF -DGMX_PREFER_STATIC_LIBS=ON
> > -DCMAKE_C_FLAGS="-O3 -qsmp=omp -qarch=qp -qtune=qp"
> > -DCMAKE_INSTALL_PREFIX=/gpfs/vesta-home/ikosh/gromacs-5.1.1/install
> >
> > --output  just the error:
> > -- Looking for xmlTextWriterEndAttribute in
> > /home/ikosh/programs/autotools-bin/lib/libxml2.a
> > -- Looking for xmlTextWriterEndAttribute in
> > /home/ikosh/programs/autotools-bin/lib/libxml2.a - not found
> > CMake Warning at CMakeLists.txt:543 (message):
> >   libxml2 not found.  Will build GROMACS without unit-tests.  This is not
> >   recommended, because the unit-tests help to verify that GROMACS
> functions
> >   correctly.  Most likely you are missing the libxml2-dev(el) package.
> > After
> >   you installed it, set GMX_BUILD_UNITTESTS=ON.
> >
> > Looking at the CMakeError.log in CMakeFiles:
> > /soft/buildtools/cmake/3.3.0/bin/cmake -E cmake_link_script
> > CMakeFiles/cmTC_09bc5.dir/link.txt --verbose=1
> > /soft/compilers/wrappers/xl/mpixlc_r  -Wl,-relax -O3 -qsmp=omp -qarch=qp
> > -qtune=qp -qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-03
> > 0 -qlanglvl=extc99 -qarch=auto -qtune=auto
> > -DCHECK_FUNCTION_EXISTS=xmlTextWriterEndAttribute
> > CMakeFiles/cmTC_09bc5.dir/CheckFunctionExist
> > s.c.o  -o cmTC_09bc5  /home/ikosh/programs/autotools-bin/lib/libxml2.a
> > /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> > `xmlGzfileOpenW':
> > /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1275: undefined reference to
> > `gzopen64'
> > /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1246: undefined reference to
> > `gzdopen'
> > 

Re: [gmx-users] Choosing Parameter values of PTMs

[Laercio Pol Fachin]

Hi, 
If you're planning to use GROMOS parameters set, please take a look at the 
following publications, about GROMOS 53A6glyc:
http://pubs.acs.org/doi/pdf/10.1021/ct300479h
http://onlinelibrary.wiley.com/store/10.1002/jcc.23721/asset/jcc23721.pdf;jsessionid=10781A1F0B927C8F5B1C7DB43FB5C856.f04t03?v=1=ikikyyfp=abdd9c6763f6a62c815d1add4b4fce41504c92e2
Best regards,Laercio Pol Fachin

Em Quinta-feira, 11 de Fevereiro de 2016 13:17, 
"gromacs.org_gmx-users-requ...@maillist.sys.kth.se" 
 escreveu:
 

 Send gromacs.org_gmx-users mailing list submissions to
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Today's Topics:

  1. View Trajectory - Water Expansion (Natalie Stephenson)
  2. Re: View Trajectory - Water Expansion (Justin Lemkul)
  3. Choosing Parameter values of PTMs (David Newman)
  4. Re: Choosing Parameter values of PTMs (bipin singh)
  5. Re: Choosing Parameter values of PTMs (Krzysztof Kuczera)


--

Message: 3
Date: Thu, 11 Feb 2016 12:59:41 +
From: David Newman 
To: "gromacs.org_gmx-users@maillist.sys.kth.se"
    
Subject: [gmx-users] Choosing Parameter values of PTMs
Message-ID:
    

    
Content-Type: text/plain; charset="iso-8859-1"

Hi all,

I'm starting a MD project using gromacs and we're looking to expand on the 
previous work in the lab modelling our receptors of interest by looking at the 
effects of gylcosylation. Is there a current best standard for parameters for 
modelling glycans?

Thanks,


--

-- 
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[gmx-users] gromacs-5.1.1 installation error: libxml2 problem

[Irina Kosheleva]

Dear gmx-users.
I would like to install gromacs-5.1.1 on a cluster where I have only user 
privileges. The machine has arch linux-rhel_6-ppc64.
I would like to install it with unittest support thus I need libxml2.a compiled 
library.
The cluster does not have this library installed so I have downloaded 
libxml2-2.9.2 and compiled it with zlib support:
 ./configure --prefix=/home/ikosh/programs/autotools-bin 
--with-python-install-dir=/home/ikosh/programs/autotools-bin 
--with-zlib=/soft/libraries/alcf/current/xl/ZLIB

Now, I would like to use this static libxml2.a library to compile gromacs-5.1.1:
cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r 
-DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX 
-DFFTWF_INCLUDE_DIR=/soft/libraries/alcf/current/xl/FFTW3/include 
-DFFTWF_LIBRARY=/soft/libraries/alcf/current/xl/FFTW3/lib/libfftw3f.a 
-DLIBXML2_INCLUDE_DIR=/gpfs/vesta-home/ikosh/programs/autotools-bin/include  
-DLIBXML2_LIBRARIES=/gpfs/vesta-home/ikosh/programs/autotools-bin/lib/libxml2.a 
-DZLIB_INCLUDE_DIR=/soft/libraries/soft/libraries/alcf/current/xl/ZLIB/include 
-DZLIB=/soft/libraries/alcf/current/xl/ZLIB/lib/libz.a
-DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF -DGMX_PREFER_STATIC_LIBS=ON  
-DCMAKE_C_FLAGS="-O3 -qsmp=omp -qarch=qp -qtune=qp" 
-DCMAKE_INSTALL_PREFIX=/gpfs/vesta-home/ikosh/gromacs-5.1.1/install

--output  just the error:
-- Looking for xmlTextWriterEndAttribute in 
/home/ikosh/programs/autotools-bin/lib/libxml2.a
-- Looking for xmlTextWriterEndAttribute in 
/home/ikosh/programs/autotools-bin/lib/libxml2.a - not found
CMake Warning at CMakeLists.txt:543 (message):
  libxml2 not found.  Will build GROMACS without unit-tests.  This is not
  recommended, because the unit-tests help to verify that GROMACS functions
  correctly.  Most likely you are missing the libxml2-dev(el) package.  After
  you installed it, set GMX_BUILD_UNITTESTS=ON.

Looking at the CMakeError.log in CMakeFiles:
/soft/buildtools/cmake/3.3.0/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_09bc5.dir/link.txt --verbose=1
/soft/compilers/wrappers/xl/mpixlc_r  -Wl,-relax -O3 -qsmp=omp -qarch=qp 
-qtune=qp -qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-03
0 -qlanglvl=extc99 -qarch=auto -qtune=auto  
-DCHECK_FUNCTION_EXISTS=xmlTextWriterEndAttribute
CMakeFiles/cmTC_09bc5.dir/CheckFunctionExist
s.c.o  -o cmTC_09bc5  /home/ikosh/programs/autotools-bin/lib/libxml2.a
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileOpenW':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1275: undefined reference to 
`gzopen64'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1246: undefined reference to 
`gzdopen'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`__xmlParserInputBufferCreateFilename':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:2670: undefined reference to 
`gzdirect'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlFreeZMemBuff':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1556: undefined reference to 
`deflateEnd'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileOpen_real':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1167: undefined reference to 
`gzdopen'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1198: undefined reference to 
`gzopen64'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileClose':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1331: undefined reference to 
`gzclose'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileWrite':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1315: undefined reference to 
`gzwrite'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlZMemBuffGetContent':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1758: undefined reference to 
`deflate'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlZMemBuffAppend':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1717: undefined reference to 
`deflate'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1729: undefined reference to `crc32'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileRead':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1295: undefined reference to `gzread'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlCreateZMemBuff':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1600: undefined reference to 
`deflateInit2_'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1615: undefined reference to `crc32'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(nanohttp.o): In function 
`xmlNanoHTTPFreeCtxt':
/home/ikosh/programs/libxml2-2.9.3/nanohttp.c:432: undefined reference to 
`inflateEnd'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(nanohttp.o): In function 
`xmlNanoHTTPRead':
/home/ikosh/programs/libxml2-2.9.3/nanohttp.c:1292: undefined reference to 
`inflate'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(nanohttp.o): In function 
`xmlNanoHTTPScanAnswer':

Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

[Smith, Micholas D.]

Quick clarifying question, are you sure you have the development version of the 
libxml2 package (the source with the headers and everything)?

Also this might be a good time to complain to your sys-admin to install the 
libxml2-dev library, as it is used in a lot of other programs too, and you 
would just be saving everyone a headache.


===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Irina 
Kosheleva 
Sent: Thursday, February 11, 2016 12:08 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] gromacs-5.1.1 installation error:  libxml2 problem

Dear gmx-users.
I would like to install gromacs-5.1.1 on a cluster where I have only user 
privileges. The machine has arch linux-rhel_6-ppc64.
I would like to install it with unittest support thus I need libxml2.a compiled 
library.
The cluster does not have this library installed so I have downloaded 
libxml2-2.9.2 and compiled it with zlib support:
 ./configure --prefix=/home/ikosh/programs/autotools-bin 
--with-python-install-dir=/home/ikosh/programs/autotools-bin 
--with-zlib=/soft/libraries/alcf/current/xl/ZLIB

Now, I would like to use this static libxml2.a library to compile gromacs-5.1.1:
cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r 
-DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX 
-DFFTWF_INCLUDE_DIR=/soft/libraries/alcf/current/xl/FFTW3/include 
-DFFTWF_LIBRARY=/soft/libraries/alcf/current/xl/FFTW3/lib/libfftw3f.a 
-DLIBXML2_INCLUDE_DIR=/gpfs/vesta-home/ikosh/programs/autotools-bin/include  
-DLIBXML2_LIBRARIES=/gpfs/vesta-home/ikosh/programs/autotools-bin/lib/libxml2.a 
-DZLIB_INCLUDE_DIR=/soft/libraries/soft/libraries/alcf/current/xl/ZLIB/include 
-DZLIB=/soft/libraries/alcf/current/xl/ZLIB/lib/libz.a
-DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF -DGMX_PREFER_STATIC_LIBS=ON  
-DCMAKE_C_FLAGS="-O3 -qsmp=omp -qarch=qp -qtune=qp" 
-DCMAKE_INSTALL_PREFIX=/gpfs/vesta-home/ikosh/gromacs-5.1.1/install

--output  just the error:
-- Looking for xmlTextWriterEndAttribute in 
/home/ikosh/programs/autotools-bin/lib/libxml2.a
-- Looking for xmlTextWriterEndAttribute in 
/home/ikosh/programs/autotools-bin/lib/libxml2.a - not found
CMake Warning at CMakeLists.txt:543 (message):
  libxml2 not found.  Will build GROMACS without unit-tests.  This is not
  recommended, because the unit-tests help to verify that GROMACS functions
  correctly.  Most likely you are missing the libxml2-dev(el) package.  After
  you installed it, set GMX_BUILD_UNITTESTS=ON.

Looking at the CMakeError.log in CMakeFiles:
/soft/buildtools/cmake/3.3.0/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_09bc5.dir/link.txt --verbose=1
/soft/compilers/wrappers/xl/mpixlc_r  -Wl,-relax -O3 -qsmp=omp -qarch=qp 
-qtune=qp -qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-03
0 -qlanglvl=extc99 -qarch=auto -qtune=auto  
-DCHECK_FUNCTION_EXISTS=xmlTextWriterEndAttribute
CMakeFiles/cmTC_09bc5.dir/CheckFunctionExist
s.c.o  -o cmTC_09bc5  /home/ikosh/programs/autotools-bin/lib/libxml2.a
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileOpenW':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1275: undefined reference to 
`gzopen64'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1246: undefined reference to 
`gzdopen'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`__xmlParserInputBufferCreateFilename':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:2670: undefined reference to 
`gzdirect'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlFreeZMemBuff':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1556: undefined reference to 
`deflateEnd'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileOpen_real':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1167: undefined reference to 
`gzdopen'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1198: undefined reference to 
`gzopen64'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileClose':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1331: undefined reference to 
`gzclose'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileWrite':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1315: undefined reference to 
`gzwrite'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlZMemBuffGetContent':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1758: undefined reference to 
`deflate'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlZMemBuffAppend':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1717: undefined reference to 
`deflate'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1729: undefined reference to `crc32'

Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

[Mark Abraham]

Hi,

IIRC ALCF does make available libxml2 with headers for bgq on Vesta, so I'm
sure the have/will on Mira too! Ask them.

Mark

On Thu, 11 Feb 2016 18:33 Smith, Micholas D.  wrote:

> Quick clarifying question, are you sure you have the development version
> of the libxml2 package (the source with the headers and everything)?
>
> Also this might be a good time to complain to your sys-admin to install
> the libxml2-dev library, as it is used in a lot of other programs too, and
> you would just be saving everyone a headache.
>
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Irina
> Kosheleva 
> Sent: Thursday, February 11, 2016 12:08 PM
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] gromacs-5.1.1 installation error:  libxml2 problem
>
> Dear gmx-users.
> I would like to install gromacs-5.1.1 on a cluster where I have only user
> privileges. The machine has arch linux-rhel_6-ppc64.
> I would like to install it with unittest support thus I need libxml2.a
> compiled library.
> The cluster does not have this library installed so I have downloaded
> libxml2-2.9.2 and compiled it with zlib support:
>  ./configure --prefix=/home/ikosh/programs/autotools-bin
> --with-python-install-dir=/home/ikosh/programs/autotools-bin
> --with-zlib=/soft/libraries/alcf/current/xl/ZLIB
>
> Now, I would like to use this static libxml2.a library to compile
> gromacs-5.1.1:
> cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r
> -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX
> -DFFTWF_INCLUDE_DIR=/soft/libraries/alcf/current/xl/FFTW3/include
> -DFFTWF_LIBRARY=/soft/libraries/alcf/current/xl/FFTW3/lib/libfftw3f.a
> -DLIBXML2_INCLUDE_DIR=/gpfs/vesta-home/ikosh/programs/autotools-bin/include
> -DLIBXML2_LIBRARIES=/gpfs/vesta-home/ikosh/programs/autotools-bin/lib/libxml2.a
> -DZLIB_INCLUDE_DIR=/soft/libraries/soft/libraries/alcf/current/xl/ZLIB/include
> -DZLIB=/soft/libraries/alcf/current/xl/ZLIB/lib/libz.a
> -DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF -DGMX_PREFER_STATIC_LIBS=ON
> -DCMAKE_C_FLAGS="-O3 -qsmp=omp -qarch=qp -qtune=qp"
> -DCMAKE_INSTALL_PREFIX=/gpfs/vesta-home/ikosh/gromacs-5.1.1/install
>
> --output  just the error:
> -- Looking for xmlTextWriterEndAttribute in
> /home/ikosh/programs/autotools-bin/lib/libxml2.a
> -- Looking for xmlTextWriterEndAttribute in
> /home/ikosh/programs/autotools-bin/lib/libxml2.a - not found
> CMake Warning at CMakeLists.txt:543 (message):
>   libxml2 not found.  Will build GROMACS without unit-tests.  This is not
>   recommended, because the unit-tests help to verify that GROMACS functions
>   correctly.  Most likely you are missing the libxml2-dev(el) package.
> After
>   you installed it, set GMX_BUILD_UNITTESTS=ON.
>
> Looking at the CMakeError.log in CMakeFiles:
> /soft/buildtools/cmake/3.3.0/bin/cmake -E cmake_link_script
> CMakeFiles/cmTC_09bc5.dir/link.txt --verbose=1
> /soft/compilers/wrappers/xl/mpixlc_r  -Wl,-relax -O3 -qsmp=omp -qarch=qp
> -qtune=qp -qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-03
> 0 -qlanglvl=extc99 -qarch=auto -qtune=auto
> -DCHECK_FUNCTION_EXISTS=xmlTextWriterEndAttribute
> CMakeFiles/cmTC_09bc5.dir/CheckFunctionExist
> s.c.o  -o cmTC_09bc5  /home/ikosh/programs/autotools-bin/lib/libxml2.a
> /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> `xmlGzfileOpenW':
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1275: undefined reference to
> `gzopen64'
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1246: undefined reference to
> `gzdopen'
> /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> `__xmlParserInputBufferCreateFilename':
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:2670: undefined reference to
> `gzdirect'
> /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> `xmlFreeZMemBuff':
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1556: undefined reference to
> `deflateEnd'
> /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> `xmlGzfileOpen_real':
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1167: undefined reference to
> `gzdopen'
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1198: undefined reference to
> `gzopen64'
> /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> `xmlGzfileClose':
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1331: undefined reference to
> `gzclose'
> /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> `xmlGzfileWrite':
> /home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1315: undefined reference to
> `gzwrite'
> /home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function
> `xmlZMemBuffGetContent':
> 

[gmx-users] CTP .gro and .itp file

[Mohsen Ramezanpour]

Dear All,

I am interested in doing MD simulation on protein and CTP molecule,
preferably in amber99sb-ildn ff in Gromacs. Well, I think we can also use
GAFF for CTP in combination with amber99-sb-ildn for protein. Please
correct me if I am wrong.

There are parameter files for ATP and GTP in .prep and .frcmod formats in
http://www.pharmacy.manchester.ac.uk/bryce/amber.
I have also .prep and .frcmod files for CTP from a published work.

I found relevant useful discussions in mailing list, for ATP though:
adding ATP parms to AMBER99

by
Stephen(2014-04-11),
acetonitrile from amber to gromacs
 by
Vedat (2010-05-19),
ATP for

by
Chandan ( 2010-02-05).

However, before going through all file transform process between amber and
Gromacs, I was wondering if there is any parameter file (.gro and .itp)
available for CTP around or if there is any database I can find there.

Thanks in advance for your comments
Cheers
Mohsen




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