Re: [gmx-users] Material science

[Mark Abraham]

Hi,

Yes, but only if your model uses only pairwise potentials. So no EAM, etc.

Mark

On Fri, Dec 9, 2016 at 5:25 PM RAHUL SURESH  wrote:

> Hi
>
> Is it possible to do dynamic studies for materials like graphene, silicene,
> etc in gromacs.
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[gmx-users] xtc to dcd conversion

[Amir Zeb]

Hi
How can I convert xtc file of trajectory to dcd file for dccm analysis?

Thanks
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[gmx-users] Regarding error in hydrogen bond lifetime

[Apramita Chand]

Dear All,
I'm trying to calculate the hydrogen bond lifetime in my system
(water-ethanol) using command g_hbond -f traj.trr -s md.tpr  -n index.ndx
-ac -life hblife.xvg. It is peculiar to note that when I select index
groups as OW and HW (for water), it finds 0 hydrogen bonds! But when I
select water and water from the index file, it shows the hydrogen bond
lifetime to be















































*Select a group: 15Selected 15: 'Water'Select a group: 15Selected 15:
'Water'Calculating hydrogen bonds in Water (2892 atoms)Found 964 donors and
964 acceptorsMaking hbmap structure...done.trn version: GMX_trn_file
(single precision)Reading frame   0 time0.000   Will do grid-seach
on 8x8x8 grid, rcut=0.35Last frame  15000 time 15000.000   Found 453844
different hydrogen bonds in trajectoryFound 460098 different atom-pairs
within hydrogen bonding distanceMerging hbonds with Acceptor and Donor
swapped964/964- Reduced number of hbonds from 453844 to 453844- Reduced
number of distances from 460098 to 460098Back Off! I just backed up
hbnum.xvg to ./#hbnum.xvg.2#Average number of hbonds per timeframe 1498.831
out of 464648 possible PLEASE READ AND CITE THE FOLLOWING REFERENCE
D. van der Spoel, P. J. van Maaren, P. Larsson and N.
TimneanuThermodynamics of hydrogen bonding in hydrophilic and hydrophobic
mediaJ. Phys. Chem. B 110 (2006) pp. 4393-4398  --- Thank
You ---  Doing autocorrelation according to the theory of
Luzar and Chandler.ACF 453844/453844Normalization for c(t) = 0.000667222
for gh(t) = 4.44762e-08Back Off! I just backed up hbac.xvg to
./#hbac.xvg.2#Hydrogen bond thermodynamics at T = 298.15 KFitting
parameters chi^2 = 0.00780548Q =
0--Type  Rate (1/ps)
Time (ps)  DG (kJ/mol)  Chi^2Forward 0.201  4.968   8.502
0.00780548Backward0.530  1.885   6.100One-way
0.208  4.817   8.425Integral0.069 14.445
11.148Relaxation  0.119  8.377   9.797Back Off! I just backed
up h_w.vg.xvg to ./#h_w.vg.xvg.1#HB lifetime = 3.50 psNote that the
lifetime obtained in this manner is close to uselessUse the -ac option
instead and check the Forward lifetime*.


So , is the forward lifetime 4.968 or 3.50 ps? Also, should I divide the
value by 2 since there are two hydrogens in water ?

Next, in water-ethanol hydrogen bonds, if I give the groups as Oethanol and
water, and OW , ethanol   , I get different lifetimes but get fatal error
as no 'hydrogen bonds' if I try specifying the exact two sites like
OW-HEthanol or Oethanol-HW1.
Why is this happening?


Regards,
Apramita
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Re: [gmx-users] Force field for phosphorylated residues

[Mark Abraham]

Hi,

What atoms do you have in that residue, what's in the c.tdb and .rtp for
GLN in force field and what did you choose for termini?

Mark

On Fri, Dec 9, 2016 at 4:05 PM Seera Suryanarayana 
wrote:

> Dear gromacs users,
>
>  I have one protein with phosphoserine and phosphothreonine. I want to
>  do simulation, but I do not know which force field I have to use. None
>  of the force field from gromacs has the information of phospho
>  residues. Then I tried with charm36, but did work. Kindly suggest me
>  what I can do.
>
>
> Well, CHARMM36 has everything you need included, so unless you explain
> what "didnot work" means (because it's the single most useless phrase
> in debugging
> anything), there's little anyone can do to help you.  Please describe
> exactly what the problem was (commands, output, errors, etc).
>
> -Justin
>
>
>
> Dear Justin,
>
> I solved the problem. That is only the mismatching of residue names
> and I renamed the residues in my PDB file. Now the problem is with OXT
> atom at C-terminal end.I other words the exact error is "Atom OXT in
> residue GLN 68 was not found in rtp entry GLN with 17 atoms while
> sorting the atoms ". I understood the error. rtp file does not  have
> the atom OXT information. How could one solve this problem?
>
> Thanks in advance
>
> Surya
> Graduate student
> India.
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[gmx-users] Force field for phosphorylated residues

[Seera Suryanarayana]

Dear gromacs users,

 I have one protein with phosphoserine and phosphothreonine. I want to
 do simulation, but I do not know which force field I have to use. None
 of the force field from gromacs has the information of phospho
 residues. Then I tried with charm36, but did work. Kindly suggest me
 what I can do.


Well, CHARMM36 has everything you need included, so unless you explain
what "didnot work" means (because it's the single most useless phrase
in debugging
anything), there's little anyone can do to help you.  Please describe
exactly what the problem was (commands, output, errors, etc).

-Justin



Dear Justin,

I solved the problem. That is only the mismatching of residue names
and I renamed the residues in my PDB file. Now the problem is with OXT
atom at C-terminal end.I other words the exact error is "Atom OXT in
residue GLN 68 was not found in rtp entry GLN with 17 atoms while
sorting the atoms ". I understood the error. rtp file does not  have
the atom OXT information. How could one solve this problem?

Thanks in advance

Surya
Graduate student
India.
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Re: [gmx-users] Character issues

[Justin Lemkul]

On 12/8/16 2:43 PM, Kelsy Yuan wrote:

Hi Mark,

Sorry for the confusion. The command I use is: grompp -p topol.top -f
engmin.mdp -c 16+mica.gro -zero, I want to do the energy minimization for
my system that contains 16 stearic acid and a mica surface. I checked all
my input files as well as the force field files, there is no such line.
Following is the terminal output:
---
Program grompp, VERSION 5.0.6
Source code file:
/usr/local/src/gromacs-5.0.6/src/gromacs/utility/cstringutil.c, line: 112

Fatal error:
An input file contains a line longer than 4095 characters, while the buffer
passed to fgets2 has size 4095. The line starts with: '1 AL1 1
  UNL A2'  ay1
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---



The input files that grompp reads are whatever you pass to it on the command 
line (.gro, .top, and .mdp) and the force field files.  Since this must be a 
custom force field, there are many potential places for problems, but something 
you created/edited must contain this line.  grompp doesn't do anything it's not 
told.


If you need further help, you'll have to upload all of your files (everything 
listed above) to a file-sharing service and provide a link.


Note that using -zero is potentially dangerous.  If your force field is missing 
interactions and you're just trying to get past them, that may generate an 
unstable system.


-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] Character issues

[Mark Abraham]

Hi,

That's the end of the terminal output. What came before it is a clue.

Mark

On Fri, 9 Dec 2016 06:44 Kelsy Yuan  wrote:

> Hi Mark,
>
> Sorry for the confusion. The command I use is: grompp -p topol.top -f
> engmin.mdp -c 16+mica.gro -zero, I want to do the energy minimization for
> my system that contains 16 stearic acid and a mica surface. I checked all
> my input files as well as the force field files, there is no such line.
> Following is the terminal output:
> ---
> Program grompp, VERSION 5.0.6
> Source code file:
> /usr/local/src/gromacs-5.0.6/src/gromacs/utility/cstringutil.c, line: 112
>
> Fatal error:
> An input file contains a line longer than 4095 characters, while the buffer
> passed to fgets2 has size 4095. The line starts with: '1 AL1 1
>   UNL A2'  ay1
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> Thanks for trying to help,
> Kelsy
>
> On 8 December 2016 at 11:06, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Which of your files has that line, and why is it so long? You aren't
> > sharing useful things like your command line and the terminal output, so
> > it's hard to say anything useful.
> >
> > Mark
> >
> > On Fri, 9 Dec 2016 05:52 Kelsy Yuan  wrote:
> >
> > > Hi Mark,
> > >
> > > Thanks for your quick reply. I tried to use Gromacs 5.0.6 to grompp, it
> > did
> > > give me a little bit more information about the error, without
> mentioning
> > > "20s". However, I cannot find the exact position since I don't have
> that
> > > line in my input file. There is not much information about it on the
> > > website nor manual. I wonder is it possible to get some further
> > > explanations? Thank you in advance.
> > >
> > > ---
> > > Program grompp, VERSION 5.0.6
> > > Source code file:
> > > /usr/local/src/gromacs-5.0.6/src/gromacs/utility/cstringutil.c, line:
> > 112
> > >
> > > Fatal error:
> > > An input file contains a line longer than 4095 characters, while the
> > buffer
> > > passed to fgets2 has size 4095. The line starts with: '1 AL1 1
> > >   UNL A2'  ay1
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > > ---
> > >
> > >
> > > Sincerely,
> > > Kelsy
> > >
> > > On 2 December 2016 at 14:52, Mark Abraham 
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > What makes you think "_" is more relevant than "20s"?
> > > >
> > > > You could well have a better experience if you were not using a
> version
> > > of
> > > > software that is five years old.
> > > >
> > > > Matk
> > > >
> > > > On Fri, 2 Dec 2016 22:45 Kelsy Yuan  wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I am trying to do an energy minimization of my system that contains
> > > > stearic
> > > > > acid molecules and an ionic surface. Every time I grompp I get the
> > > > > following error massage:
> > > > >
> > > > > Program grompp_s_mpi, VERSION 4.5.5
> > > > > Source code file: string2.c, line: 105
> > > > >
> > > > > Fatal error:
> > > > > An input file contains a line longer than 4095 characters, while
> the
> > > > buffer
> > > > > passed to fgets2 has size 4095. The line starts with: '20s'
> > > > > For more information and tips for troubleshooting, please check the
> > > > GROMACS
> > > > > website at http://www.gromacs.org/Documentation/Errors
> > > > >
> > > > >
> > > > > I checked every single input file as well as the force filed
> > directory,
> > > > > none of them contains "_" when I viewed them on different text
> > > editors. I
> > > > > wonder does anyone know another solution or possible reasons for
> this
> > > > > issue?
> > > > >
> > > > > Thank you in advance,
> > > > > Kelsy
> > > > > --
> > > > > 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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> > > > Support/Mailing_Lists/GMX-Users_List before posting!
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> or
> > > > send a mail to 

Re: [gmx-users] Character issues

[Kelsy Yuan]

Hi Mark,

Sorry for the confusion. The command I use is: grompp -p topol.top -f
engmin.mdp -c 16+mica.gro -zero, I want to do the energy minimization for
my system that contains 16 stearic acid and a mica surface. I checked all
my input files as well as the force field files, there is no such line.
Following is the terminal output:
---
Program grompp, VERSION 5.0.6
Source code file:
/usr/local/src/gromacs-5.0.6/src/gromacs/utility/cstringutil.c, line: 112

Fatal error:
An input file contains a line longer than 4095 characters, while the buffer
passed to fgets2 has size 4095. The line starts with: '1 AL1 1
  UNL A2'  ay1
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Thanks for trying to help,
Kelsy

On 8 December 2016 at 11:06, Mark Abraham  wrote:

> Hi,
>
> Which of your files has that line, and why is it so long? You aren't
> sharing useful things like your command line and the terminal output, so
> it's hard to say anything useful.
>
> Mark
>
> On Fri, 9 Dec 2016 05:52 Kelsy Yuan  wrote:
>
> > Hi Mark,
> >
> > Thanks for your quick reply. I tried to use Gromacs 5.0.6 to grompp, it
> did
> > give me a little bit more information about the error, without mentioning
> > "20s". However, I cannot find the exact position since I don't have that
> > line in my input file. There is not much information about it on the
> > website nor manual. I wonder is it possible to get some further
> > explanations? Thank you in advance.
> >
> > ---
> > Program grompp, VERSION 5.0.6
> > Source code file:
> > /usr/local/src/gromacs-5.0.6/src/gromacs/utility/cstringutil.c, line:
> 112
> >
> > Fatal error:
> > An input file contains a line longer than 4095 characters, while the
> buffer
> > passed to fgets2 has size 4095. The line starts with: '1 AL1 1
> >   UNL A2'  ay1
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > ---
> >
> >
> > Sincerely,
> > Kelsy
> >
> > On 2 December 2016 at 14:52, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > What makes you think "_" is more relevant than "20s"?
> > >
> > > You could well have a better experience if you were not using a version
> > of
> > > software that is five years old.
> > >
> > > Matk
> > >
> > > On Fri, 2 Dec 2016 22:45 Kelsy Yuan  wrote:
> > >
> > > > Hi,
> > > >
> > > > I am trying to do an energy minimization of my system that contains
> > > stearic
> > > > acid molecules and an ionic surface. Every time I grompp I get the
> > > > following error massage:
> > > >
> > > > Program grompp_s_mpi, VERSION 4.5.5
> > > > Source code file: string2.c, line: 105
> > > >
> > > > Fatal error:
> > > > An input file contains a line longer than 4095 characters, while the
> > > buffer
> > > > passed to fgets2 has size 4095. The line starts with: '20s'
> > > > For more information and tips for troubleshooting, please check the
> > > GROMACS
> > > > website at http://www.gromacs.org/Documentation/Errors
> > > >
> > > >
> > > > I checked every single input file as well as the force filed
> directory,
> > > > none of them contains "_" when I viewed them on different text
> > editors. I
> > > > wonder does anyone know another solution or possible reasons for this
> > > > issue?
> > > >
> > > > Thank you in advance,
> > > > Kelsy
> > > > --
> > > > 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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> > > Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] Character issues

[Mark Abraham]

Hi,

Which of your files has that line, and why is it so long? You aren't
sharing useful things like your command line and the terminal output, so
it's hard to say anything useful.

Mark

On Fri, 9 Dec 2016 05:52 Kelsy Yuan  wrote:

> Hi Mark,
>
> Thanks for your quick reply. I tried to use Gromacs 5.0.6 to grompp, it did
> give me a little bit more information about the error, without mentioning
> "20s". However, I cannot find the exact position since I don't have that
> line in my input file. There is not much information about it on the
> website nor manual. I wonder is it possible to get some further
> explanations? Thank you in advance.
>
> ---
> Program grompp, VERSION 5.0.6
> Source code file:
> /usr/local/src/gromacs-5.0.6/src/gromacs/utility/cstringutil.c, line: 112
>
> Fatal error:
> An input file contains a line longer than 4095 characters, while the buffer
> passed to fgets2 has size 4095. The line starts with: '1 AL1 1
>   UNL A2'  ay1
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
>
> Sincerely,
> Kelsy
>
> On 2 December 2016 at 14:52, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > What makes you think "_" is more relevant than "20s"?
> >
> > You could well have a better experience if you were not using a version
> of
> > software that is five years old.
> >
> > Matk
> >
> > On Fri, 2 Dec 2016 22:45 Kelsy Yuan  wrote:
> >
> > > Hi,
> > >
> > > I am trying to do an energy minimization of my system that contains
> > stearic
> > > acid molecules and an ionic surface. Every time I grompp I get the
> > > following error massage:
> > >
> > > Program grompp_s_mpi, VERSION 4.5.5
> > > Source code file: string2.c, line: 105
> > >
> > > Fatal error:
> > > An input file contains a line longer than 4095 characters, while the
> > buffer
> > > passed to fgets2 has size 4095. The line starts with: '20s'
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > >
> > >
> > > I checked every single input file as well as the force filed directory,
> > > none of them contains "_" when I viewed them on different text
> editors. I
> > > wonder does anyone know another solution or possible reasons for this
> > > issue?
> > >
> > > Thank you in advance,
> > > Kelsy
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [gmx-users] Character issues

[Kelsy Yuan]

Hi Mark,

Thanks for your quick reply. I tried to use Gromacs 5.0.6 to grompp, it did
give me a little bit more information about the error, without mentioning
"20s". However, I cannot find the exact position since I don't have that
line in my input file. There is not much information about it on the
website nor manual. I wonder is it possible to get some further
explanations? Thank you in advance.

---
Program grompp, VERSION 5.0.6
Source code file:
/usr/local/src/gromacs-5.0.6/src/gromacs/utility/cstringutil.c, line: 112

Fatal error:
An input file contains a line longer than 4095 characters, while the buffer
passed to fgets2 has size 4095. The line starts with: '1 AL1 1
  UNL A2'  ay1
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


Sincerely,
Kelsy

On 2 December 2016 at 14:52, Mark Abraham  wrote:

> Hi,
>
> What makes you think "_" is more relevant than "20s"?
>
> You could well have a better experience if you were not using a version of
> software that is five years old.
>
> Matk
>
> On Fri, 2 Dec 2016 22:45 Kelsy Yuan  wrote:
>
> > Hi,
> >
> > I am trying to do an energy minimization of my system that contains
> stearic
> > acid molecules and an ionic surface. Every time I grompp I get the
> > following error massage:
> >
> > Program grompp_s_mpi, VERSION 4.5.5
> > Source code file: string2.c, line: 105
> >
> > Fatal error:
> > An input file contains a line longer than 4095 characters, while the
> buffer
> > passed to fgets2 has size 4095. The line starts with: '20s'
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> >
> > I checked every single input file as well as the force filed directory,
> > none of them contains "_" when I viewed them on different text editors. I
> > wonder does anyone know another solution or possible reasons for this
> > issue?
> >
> > Thank you in advance,
> > Kelsy
> > --
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Re: [gmx-users] Vagrant 2-node slurm cluster with gromacs, mpi

[Victor Rosas Garcia]

OK, thanks.

2016-12-08 10:57 GMT-06:00 Mark Abraham :

> Hi,
>
> I literally have no idea, but I have heard from Szilard Pall that it can be
> done and runs reasonably :-)
>
> Mark
>
> On Fri, Dec 9, 2016 at 3:49 AM Victor Rosas Garcia  >
> wrote:
>
> > Interesting.
> >
> > Mark, would you mind pointing out a few resources on how to configure
> for a
> > Gigabit network? So far I have found J Comput Chem 28: 2075–2084, 2007,
> but
> > there must be something else out there.
> >
> > Victor
> >
> > 2016-12-08 10:08 GMT-06:00 Mark Abraham :
> >
> > > Hi,
> > >
> > > Thanks for the tip. I would further suggest that people consider the
> > > attributes of their network before attempting such a setup. It is
> > possible
> > > to get reasonable performance from multi-node GROMACS using Gigabit
> > > ethernet, but I would expect to have to do a lot of work configuring
> it.
> > > GROMACS performance is extremely sensitive to communication latency,
> and
> > > every extra layer of middleware hurts that.
> > >
> > > Mark
> > >
> > > On Tue, Dec 6, 2016 at 1:16 AM Jan Domanski  wrote:
> > >
> > > > Hi guys,
> > > >
> > > > While not exactly related to gromacs per-se, this may be useful to
> > folks
> > > > who want to try running gromacs with slurm out on their laptops,
> rather
> > > > than deploying on a slice of a hardware cluster.
> > > >
> > > > https://github.com/jandom/gromacs-slurm-openmpi-vagrant
> > > >
> > > > - Jan
> > > > --
> > > > 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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Re: [gmx-users] Vagrant 2-node slurm cluster with gromacs, mpi

[Mark Abraham]

Hi,

I literally have no idea, but I have heard from Szilard Pall that it can be
done and runs reasonably :-)

Mark

On Fri, Dec 9, 2016 at 3:49 AM Victor Rosas Garcia 
wrote:

> Interesting.
>
> Mark, would you mind pointing out a few resources on how to configure for a
> Gigabit network? So far I have found J Comput Chem 28: 2075–2084, 2007, but
> there must be something else out there.
>
> Victor
>
> 2016-12-08 10:08 GMT-06:00 Mark Abraham :
>
> > Hi,
> >
> > Thanks for the tip. I would further suggest that people consider the
> > attributes of their network before attempting such a setup. It is
> possible
> > to get reasonable performance from multi-node GROMACS using Gigabit
> > ethernet, but I would expect to have to do a lot of work configuring it.
> > GROMACS performance is extremely sensitive to communication latency, and
> > every extra layer of middleware hurts that.
> >
> > Mark
> >
> > On Tue, Dec 6, 2016 at 1:16 AM Jan Domanski  wrote:
> >
> > > Hi guys,
> > >
> > > While not exactly related to gromacs per-se, this may be useful to
> folks
> > > who want to try running gromacs with slurm out on their laptops, rather
> > > than deploying on a slice of a hardware cluster.
> > >
> > > https://github.com/jandom/gromacs-slurm-openmpi-vagrant
> > >
> > > - Jan
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
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Re: [gmx-users] Vagrant 2-node slurm cluster with gromacs, mpi

[Victor Rosas Garcia]

Interesting.

Mark, would you mind pointing out a few resources on how to configure for a
Gigabit network? So far I have found J Comput Chem 28: 2075–2084, 2007, but
there must be something else out there.

Victor

2016-12-08 10:08 GMT-06:00 Mark Abraham :

> Hi,
>
> Thanks for the tip. I would further suggest that people consider the
> attributes of their network before attempting such a setup. It is possible
> to get reasonable performance from multi-node GROMACS using Gigabit
> ethernet, but I would expect to have to do a lot of work configuring it.
> GROMACS performance is extremely sensitive to communication latency, and
> every extra layer of middleware hurts that.
>
> Mark
>
> On Tue, Dec 6, 2016 at 1:16 AM Jan Domanski  wrote:
>
> > Hi guys,
> >
> > While not exactly related to gromacs per-se, this may be useful to folks
> > who want to try running gromacs with slurm out on their laptops, rather
> > than deploying on a slice of a hardware cluster.
> >
> > https://github.com/jandom/gromacs-slurm-openmpi-vagrant
> >
> > - Jan
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] parallel processing

[Mark Abraham]

Hi,

On Sat, Dec 3, 2016 at 6:34 PM abhisek Mondal 
wrote:

> Hello Mark,
>
> I had gone through the page. Not finding any solution there.
>
> My architecture is:
> Architecture:  x86_64
> CPU op-mode(s):32-bit, 64-bit
> Byte Order:Little Endian
> CPU(s):16
> On-line CPU(s) list:   0-15
> Thread(s) per core:1
> Core(s) per socket:8
> Socket(s): 2
> NUMA node(s):  2
> Vendor ID: GenuineIntel
> CPU family:6
> Model: 45
> Stepping:  7
> CPU MHz:   2593.616
> BogoMIPS:  5186.82
> Virtualization:VT-x
> L1d cache: 32K
> L1i cache: 32K
> L2 cache:  256K
> L3 cache:  20480K
> NUMA node0 CPU(s): 0-7
> NUMA node1 CPU(s): 8-15
>
>
> When i put "mpirun -np 64 gmx_mpi mdrun  -v -deffnm npt" it just runs on a
> single node using 64 threads (16 availavle for a single node normally).
>
> How am I supposed to do node distribution efficiently ? I'm trying to run
> the job using 4 nodes and 16 threads.
> A little suggestion would be highly appreciated.
>

You read the documentation for your MPI library and e.g. set up a suitable
hostfile so that mpirun knows which nodes to use. mdrun doesn't know or
care how mpirun works, but mpirun has to be set up to work properly :-)

Mark


>
>
> On Fri, Dec 2, 2016 at 4:55 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Please check out
> > http://manual.gromacs.org/documentation/2016.1/user-
> > guide/mdrun-performance.html.
> > Your first sample command is woefully inefficient, but for em this likely
> > doesn't matter.
> >
> > Mark
> >
> > On Fri, 2 Dec 2016 09:01 abhisek Mondal  wrote:
> >
> > > But if I want to run the same job in 4 nodes (available cores= 4*16)
> then
> > > how would this work ?
> > >
> > > On Fri, Dec 2, 2016 at 2:20 PM,  wrote:
> > >
> > > > Hi Abhisek,
> > > >
> > > > You would need to use another version of gromacs with mpi rather than
> > > > thread-mpi (installed by adding DGMX_MPI=ON to the cmake command).
> You
> > > > could then use the following command
> > > >
> > > > mpirun -np 4 gmx_mpi mdrun -ntomp 16 -npme 0 -v -deffnm em
> > > >
> > > > I'm not sure why you are specifying -npme 0 but would suggest you
> don't
> > > do
> > > > this and instead let the number of separate pme ranks be set
> > > > automatically.
> > > >
> > > > Best wishes
> > > > James
> > > >
> > > > > Hi,
> > > > >
> > > > > I'm running gromacs on a cluster configuration as follows:
> > > > > 1 node = 16 cores
> > > > >
> > > > > I'm able to use single node with "gmx mdrun -ntmpi 4 -ntomp 16
> -npme
> > 0
> > > -v
> > > > > -deffnm em" command.
> > > > >
> > > > > How can I be able to run on multiple node (I have 20 nodes
> > available) ?
> > > > > "-nt" is not doing good here.
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Abhisek Mondal
> > > > >
> > > > > *Research Fellow*
> > > > >
> > > > > *Structural Biology and Bioinformatics Division*
> > > > > *CSIR-Indian Institute of Chemical Biology*
> > > > >
> > > > > *Kolkata 700032*
> > > > >
> > > > > *INDIA*
> > > > > --
> > > > > 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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> > or
> > > > send
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> > > > >
> > > >
> > > >
> > > > --
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> > > >
> > >
> > >
> > >
> > > --
> > > Abhisek Mondal
> > >
> > > *Research Fellow*
> > >
> > > *Structural Biology and Bioinformatics Division*
> > > *CSIR-Indian Institute of Chemical Biology*
> > >
> > > *Kolkata 700032*
> > >
> > > *INDIA*
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> > 

Re: [gmx-users] Vagrant 2-node slurm cluster with gromacs, mpi

[Mark Abraham]

Hi,

Thanks for the tip. I would further suggest that people consider the
attributes of their network before attempting such a setup. It is possible
to get reasonable performance from multi-node GROMACS using Gigabit
ethernet, but I would expect to have to do a lot of work configuring it.
GROMACS performance is extremely sensitive to communication latency, and
every extra layer of middleware hurts that.

Mark

On Tue, Dec 6, 2016 at 1:16 AM Jan Domanski  wrote:

> Hi guys,
>
> While not exactly related to gromacs per-se, this may be useful to folks
> who want to try running gromacs with slurm out on their laptops, rather
> than deploying on a slice of a hardware cluster.
>
> https://github.com/jandom/gromacs-slurm-openmpi-vagrant
>
> - Jan
> --
> 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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Re: [gmx-users] Adding external field to selected atoms

[Mark Abraham]

Hi,

On Tue, Dec 6, 2016 at 4:44 PM Bappa Ghosh  wrote:

> Dear users,
> I am trying to add an external field which will add some extra force to my
> simulation system for selected atoms.
> For that, I was following the "patching mdrun" exercise in
> http://www.gromacs.org/Developer_Zone/Programming_Guide/Patching_mdrun.
>
> There it tells to replace the function calc_f_el in
> gmx/src/mdlib/sim_util.c as follows-
>
> for(i=start; (i   if (x[i][ZZ] < box[ZZ][ZZ]/2) {
>Ext[ZZ] = FIELDFAC*Ex[ZZ].a[0]*2*x[i][ZZ]/box[ZZ][ZZ];
>   }
>   else {
>Ext[ZZ] = FIELDFAC*Ex[ZZ].a[0]*(1- 2*x[i][ZZ]/box[ZZ][ZZ]);
>   }
>   f[i][ZZ] += charge[i]*Ext[ZZ];
> }
>
> in order to add an external electric field along Z variable of the box.
>
> My questions are-
> 1. What are the variables *"start" *and *"homenr" *mean ?
>

Domains have responsibility for home atoms, but have information for a
large number of atoms with which they interact. start and homenr delimit
the range for which this domain has responsibility.


> 2. In order to add force by the external field to selected atoms, is there
> any way to select atoms from the simulation system ( may be from the
> index.ndx file ) which can be included here ?
>

There are normal .mdp options for user-defined index groups that you can
access inside modified versions of the code. e.g.
http://manual.gromacs.org/documentation/2016/user-guide/mdp-options.html#user-defined-thingies.
I would look at code for e.g. group-wise center-of-mass-motion removal to
see how to use these data structures.

Mark


> Thank you in advance.
>
>
> Best regards,
> Bappa Ghosh
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Re: [gmx-users] multi node processing issue

[Mark Abraham]

Hi,

That tends to be that your simulation is blowing up and the MPI library
isn't working out to clean up properly. Make sure your simulation runs
stably in a simple run setup, first.

Mark

On Thu, Dec 8, 2016 at 6:13 AM abhisek Mondal 
wrote:

> Hi,
>
> I'm having a hard time running a npt equilibration code with 2 nodes (32
> cores). The command I'm using is:
> mpirun -np 32 -machinefile  nodes /app/grommacs507/bin/gmx_mpi mdrun
> -tunepme -dlb auto -gcom 10 -v -deffnm npt
>
>
> But this code runs on 32 cores for sometime then  keeps running on 2-4
> cores.
>
> If you please debug me here.
>
> thanks.
>
> --
> Abhisek Mondal
>
> *Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
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Re: [gmx-users] Building using FFTW3 for FFT and MKL for BLAS/LAPACK

[Mark Abraham]

Hi,

On Fri, Dec 9, 2016 at 12:20 AM Will Furnass 
wrote:

> Hi all,
>
> I understand that FFTW3 is considered preferable to MKL for FFTs in Gromacs
> but am having difficulty getting Gromacs to compile so that it uses a
> self-built single-precision FFTW but uses the MKL for BLAS/LAPACK linear
> algebra routines.
>
> Is there a recommended way of doing this?
>

Not really. There's only a tiny fraction of GROMACS runs that use both FFT
and linear algebra, and I'd want to see some evidence that such a hybrid
ought to run faster before going to the trouble (e.g. compare relevant
component timings for all-MKL vs FFTW+whatever builds)


> FYI I'm wanting to build Gromacs 2016.1 using
>  - FFTW 3.3.5 (built by Gromacs)
>  - MKL 2017
>  - GCC 4.9.2
>  - No CUDA/MPI support (for now)
>
> I tried passing the following to cmake:
>
> -DGMX_EXTERNAL_BLAS=ON
> -DGMX_BLAS_USER=$MKLROOT/lib/intel64/libmkl_intel_lp64.a
>
> to cmake but got the following errors:
>

Per
http://manual.gromacs.org/documentation/2016/install-guide/index.html#using-mkl
there
are some further options, but your main friend is the Intel documentation
for finding out what you need for your setup - it's generally more complex
than a single static library.


>
> -- Checking that user BLAS library
>
> /usr/local/packages6/compilers/intel-ps-xe-ce/2017.0/binary/compilers_and_libraries_2017.0.098/linux/mkl/lib/intel64/libmkl_intel_lp64.a
> works
> -- Looking for dgemm_
> -- Looking for dgemm_ - not found
>

Looking at the CMakeError.log and CMakeOutput.log may prove instructive,
after you've checked the Intel docs.

Mark


> CMake Warning at cmake/gmxManageLinearAlgebraLibraries.cmake:78 (message):
>   GMX_BLAS_USER library
>
>
> /usr/local/packages6/compilers/intel-ps-xe-ce/2017.0/binary/compilers_and_libraries_2017.0.098/linux/mkl/lib/intel64/libmkl_intel_lp64.a
>   was specified, but it may not provide BLAS.  We are proceeding by
> assuming
>   you know what you are doing and that linking F77-style to this library
> will
>   work.
> Call Stack (most recent call first):
>   cmake/gmxManageLinearAlgebraLibraries.cmake:194
> (manage_linear_algebra_library)
>   cmake/gmxManageLinearAlgebraLibraries.cmake:202
> (gmxManageLinearAlgebraLibraries)
>   CMakeLists.txt:693 (include)
> -- MKL and GMX_BLAS_USER were both specified. Using the latter for BLAS.
> ...
> [100%] Linking CXX executable ../../bin/gmx
> ../../lib/libgromacs.so.2.1.0: undefined reference to `mkl_lapack_dlacpy'
> ../../lib/libgromacs.so.2.1.0: undefined reference to `mkl_blas_dcopy'
> ...
>
>
> Regards,
>
> Will
>
> --
> Dr Will Furnass | Research Computing Support Officer
> CiCS | University of Sheffield | +44 (0)114 22 23130
> http://www.sheffield.ac.uk/cics/research | http://docs.hpc.sheffield.ac.uk
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Re: [gmx-users] forcefield for phosphorylated residues

[Justin Lemkul]

On 12/8/16 4:36 AM, Seera Suryanarayana wrote:

Dear gromacs users,

I have one protein with phosphoserine and phosphothreonine. I want to
do simulation, but I do not know which force field I have to use. None
of the force field from gromacs has the information of phospho
residues. Then I tried with charm36, but did work. Kindly suggest me
what I can do.



Well, CHARMM36 has everything you need included, so unless you explain what "did 
not work" means (because it's the single most useless phrase in debugging 
anything), there's little anyone can do to help you.  Please describe exactly 
what the problem was (commands, output, errors, etc).


-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] Defining +/- in the RTP file for a molecule with 3 different molecules

[Justin Lemkul]

On 12/8/16 2:31 AM, Aishwary Shivgan wrote:

Thanks for the reply.

I will try to implement specbond in my system. Just want to ask if it could
be implemented for the following molecule having multiple branch points in
a single molecule?

http://www.sigmaaldrich.com/content/dam/sigma-aldrich/
life-science/biochemicals/migrationbiochemicals1/
complex-tetraantennary-glyc.jpg

Ultimately I want to attach the glycan to the protein.



You can probably get it to work, but it will be painful.  This is the sort of 
thing that GROMACS is admittedly not very good at doing, at least not easily.


Try http://www.charmm-gui.org/?doc=input/glycan instead.  It's designed to deal 
with complex glycosylation.  I can't remember if conversion to GROMACS format is 
included in the Glycan Reader yet, but if not, converting the topology shouldn't 
be that bad.


-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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[gmx-users] Building using FFTW3 for FFT and MKL for BLAS/LAPACK

[Will Furnass]

Hi all,

I understand that FFTW3 is considered preferable to MKL for FFTs in Gromacs
but am having difficulty getting Gromacs to compile so that it uses a
self-built single-precision FFTW but uses the MKL for BLAS/LAPACK linear
algebra routines.

Is there a recommended way of doing this?

FYI I'm wanting to build Gromacs 2016.1 using
 - FFTW 3.3.5 (built by Gromacs)
 - MKL 2017
 - GCC 4.9.2
 - No CUDA/MPI support (for now)

I tried passing the following to cmake:

-DGMX_EXTERNAL_BLAS=ON
-DGMX_BLAS_USER=$MKLROOT/lib/intel64/libmkl_intel_lp64.a

to cmake but got the following errors:

-- Checking that user BLAS library
/usr/local/packages6/compilers/intel-ps-xe-ce/2017.0/binary/compilers_and_libraries_2017.0.098/linux/mkl/lib/intel64/libmkl_intel_lp64.a
works
-- Looking for dgemm_
-- Looking for dgemm_ - not found
CMake Warning at cmake/gmxManageLinearAlgebraLibraries.cmake:78 (message):
  GMX_BLAS_USER library

/usr/local/packages6/compilers/intel-ps-xe-ce/2017.0/binary/compilers_and_libraries_2017.0.098/linux/mkl/lib/intel64/libmkl_intel_lp64.a
  was specified, but it may not provide BLAS.  We are proceeding by assuming
  you know what you are doing and that linking F77-style to this library
will
  work.
Call Stack (most recent call first):
  cmake/gmxManageLinearAlgebraLibraries.cmake:194
(manage_linear_algebra_library)
  cmake/gmxManageLinearAlgebraLibraries.cmake:202
(gmxManageLinearAlgebraLibraries)
  CMakeLists.txt:693 (include)
-- MKL and GMX_BLAS_USER were both specified. Using the latter for BLAS.
...
[100%] Linking CXX executable ../../bin/gmx
../../lib/libgromacs.so.2.1.0: undefined reference to `mkl_lapack_dlacpy'
../../lib/libgromacs.so.2.1.0: undefined reference to `mkl_blas_dcopy'
...


Regards,

Will

-- 
Dr Will Furnass | Research Computing Support Officer
CiCS | University of Sheffield | +44 (0)114 22 23130
http://www.sheffield.ac.uk/cics/research | http://docs.hpc.sheffield.ac.uk
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[gmx-users] forcefield for phosphorylated residues

[Seera Suryanarayana]

Dear gromacs users,

I have one protein with phosphoserine and phosphothreonine. I want to
do simulation, but I do not know which force field I have to use. None
of the force field from gromacs has the information of phospho
residues. Then I tried with charm36, but did work. Kindly suggest me
what I can do.

Thanks in advance
Surya
Graduate student
India.
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Re: [gmx-users] correction of pmf profile due to entropic decrease

[Erik Marklund]

Dear Alex,

No. First of all, this is taken care of by gmx wham if I remember correctly. 
And it does so by looking at the dimensionality of your umbrella sampling 
setup. Secondly, there are cases where you don’t want that correction at all. 
The manual mentions one such example. In such cases the entropic contribution 
must be removed.

Kind regards,
Erik

> On 7 Dec 2016, at 19:33, Alex  wrote:
> 
> Any suggestion please?
> Thank you.
> 
> 
> On Tue, Dec 6, 2016 at 1:16 PM, Alex  wrote:
> 
>> 
>> Hello gmx user,
>> 
>> Do we need always correct the PMF profile from US by the
>> "$k_{B}T*log[4π(\epsilon)^2]$" factor in which epsilon is reaction
>> coordinate in order to removes the entropic decrease? as been mentioned
>> here:
>> 
>> 10.1021/ct100494z
>> 
>> Hub, J. S.; de Groot, B. L.; van der Spoel, D.J. Chem. Theory
>> Comput.2010,6, 3713-3720
>> 
>> Best regards,
>> Alex
>> 
>> 
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