[gmx-users] REMD on more than one node

[YanhuaOuyang]

Hi,
I am running a REMD with grimacs 5.0, I have 46 replica, 4 nodes, 16 cores per 
node. how can I use my compute resource and what’s the command of “gmx mdrun”?
the command is below, I am not sure weather it is right
mpirun -np 4 -npme gmx mdrun -s md_01.tpr  -multi 46 -replex 500 -reseed -1.
mpirun -np 4 -npme gmx mdrun -s md_02.tpr  -multi 46 -replex 500 -reseed -1.
mpirun -np 4 -npme gmx mdrun -s md_03.tpr  -multi 46 -replex 500 -reseed -1.
…
mpirun -np 4 -npme gmx mdrun -s md_46.tpr  -multi 46 -replex 500 -reseed -1.


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Re: [gmx-users] Making separate topology file for QM atoms

[bharat gupta]

Dear Gromacs Users,

I am interested to know how to create a separate topology file for the QM
atoms of a system. It would be of great help if somebody can explain this.

For my QM system, I need to include the active site residues + ligand.

-- 
*Best Regards*
BM
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Re: [gmx-users] problem to continue MD run

[Williams Miranda]

Many thanks!

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham 
[mark.j.abra...@gmail.com]
Sent: Thursday, May 12, 2016 2:06 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] problem to continue MD run

Hi,

Yes, as you can see, the error message is refusing to append to files it
can't find, since appending is the default behaviour. If you continue with
mdrun -noappend then it will be fine. But you will now want to keep your
two sets of files separate and concatenate later with trjcat. Make a
backup, at least.

Mark

On Thu, 12 May 2016 22:01 Williams Miranda 
wrote:

> Hello
> This is the command line I am using:
>
> mpiexec mdrun_mpi -v -s step7_production.tpr  -cpi step7_production.cpt
> -deffnm step7_production
>
> and this is the error I get:
>
> Output file appending has been requested,
> but some output files listed in the checkpoint file step7_production.cpt
> are not present or are named differently by the current program:
> output files present: step7_production.log step7_production.xtc
> step7_production.edr
> output files not present or named differently: step7_production.trr
>
> ---
> Program mdrun_mpi, VERSION 5.0.6
> Source code file:
> /RQusagers/rqchpbib/stubbsda/gromacs-5.0.6/src/gromacs/gmxlib/checkpoint.c,
> line: 2640
>
> Fatal error:
> File appending requested, but 1 of the 4 output files are not present or
> are named differently
> For more information and tips for troubleshooting, please check the GROMACS
>
> Is it there any way I can continue the simulation without the *trr file?
> Thanks
> Williams
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark
> Abraham [mark.j.abra...@gmail.com]
> Sent: Thursday, May 12, 2016 1:32 AM
> To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] problem to continue MD run
>
> Hi,
>
> Please report the commands you are running, and copy and paste the error
> message. Otherwise we're just wasting time guessing :-)
>
> Mark
>
> On Thu, May 12, 2016 at 4:12 AM Williams Miranda <
> williams.mira...@ucalgary.ca> wrote:
>
> > Dear GROMACS users
> > I need to continue an unfinished simulation. Because of disk space, I
> > deleted the *trr file. Unfortunately, when I try to continue the run
> using
> > the -cpi option, gromacs complains that 1 of 4 files needed to continue
> the
> > run is missing (likely, the *trr file). What could I do?
> > Regards
> > Williams
> > --
> > 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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[gmx-users] problem to continue MD run

[Williams Miranda]

Hello
This is the command line I am using:

mpiexec mdrun_mpi -v -s step7_production.tpr  -cpi step7_production.cpt -deffnm 
step7_production

and this is the error I get:

Output file appending has been requested,
but some output files listed in the checkpoint file step7_production.cpt
are not present or are named differently by the current program:
output files present: step7_production.log step7_production.xtc 
step7_production.edr
output files not present or named differently: step7_production.trr

---
Program mdrun_mpi, VERSION 5.0.6
Source code file: 
/RQusagers/rqchpbib/stubbsda/gromacs-5.0.6/src/gromacs/gmxlib/checkpoint.c, 
line: 2640

Fatal error:
File appending requested, but 1 of the 4 output files are not present or are 
named differently
For more information and tips for troubleshooting, please check the GROMACS

Is it there any way I can continue the simulation without the *trr file?
Thanks
Williams
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Re: [gmx-users] problem to continue MD run

[Mark Abraham]

Hi,

Yes, as you can see, the error message is refusing to append to files it
can't find, since appending is the default behaviour. If you continue with
mdrun -noappend then it will be fine. But you will now want to keep your
two sets of files separate and concatenate later with trjcat. Make a
backup, at least.

Mark

On Thu, 12 May 2016 22:01 Williams Miranda 
wrote:

> Hello
> This is the command line I am using:
>
> mpiexec mdrun_mpi -v -s step7_production.tpr  -cpi step7_production.cpt
> -deffnm step7_production
>
> and this is the error I get:
>
> Output file appending has been requested,
> but some output files listed in the checkpoint file step7_production.cpt
> are not present or are named differently by the current program:
> output files present: step7_production.log step7_production.xtc
> step7_production.edr
> output files not present or named differently: step7_production.trr
>
> ---
> Program mdrun_mpi, VERSION 5.0.6
> Source code file:
> /RQusagers/rqchpbib/stubbsda/gromacs-5.0.6/src/gromacs/gmxlib/checkpoint.c,
> line: 2640
>
> Fatal error:
> File appending requested, but 1 of the 4 output files are not present or
> are named differently
> For more information and tips for troubleshooting, please check the GROMACS
>
> Is it there any way I can continue the simulation without the *trr file?
> Thanks
> Williams
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark
> Abraham [mark.j.abra...@gmail.com]
> Sent: Thursday, May 12, 2016 1:32 AM
> To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] problem to continue MD run
>
> Hi,
>
> Please report the commands you are running, and copy and paste the error
> message. Otherwise we're just wasting time guessing :-)
>
> Mark
>
> On Thu, May 12, 2016 at 4:12 AM Williams Miranda <
> williams.mira...@ucalgary.ca> wrote:
>
> > Dear GROMACS users
> > I need to continue an unfinished simulation. Because of disk space, I
> > deleted the *trr file. Unfortunately, when I try to continue the run
> using
> > the -cpi option, gromacs complains that 1 of 4 files needed to continue
> the
> > run is missing (likely, the *trr file). What could I do?
> > Regards
> > Williams
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] problem to continue MD run

[Williams Miranda]

Hello
This is the command line I am using:

mpiexec mdrun_mpi -v -s step7_production.tpr  -cpi step7_production.cpt -deffnm 
step7_production

and this is the error I get:

Output file appending has been requested,
but some output files listed in the checkpoint file step7_production.cpt
are not present or are named differently by the current program:
output files present: step7_production.log step7_production.xtc 
step7_production.edr
output files not present or named differently: step7_production.trr

---
Program mdrun_mpi, VERSION 5.0.6
Source code file: 
/RQusagers/rqchpbib/stubbsda/gromacs-5.0.6/src/gromacs/gmxlib/checkpoint.c, 
line: 2640

Fatal error:
File appending requested, but 1 of the 4 output files are not present or are 
named differently
For more information and tips for troubleshooting, please check the GROMACS

Is it there any way I can continue the simulation without the *trr file?
Thanks
Williams

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham 
[mark.j.abra...@gmail.com]
Sent: Thursday, May 12, 2016 1:32 AM
To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] problem to continue MD run

Hi,

Please report the commands you are running, and copy and paste the error
message. Otherwise we're just wasting time guessing :-)

Mark

On Thu, May 12, 2016 at 4:12 AM Williams Miranda <
williams.mira...@ucalgary.ca> wrote:

> Dear GROMACS users
> I need to continue an unfinished simulation. Because of disk space, I
> deleted the *trr file. Unfortunately, when I try to continue the run using
> the -cpi option, gromacs complains that 1 of 4 files needed to continue the
> run is missing (likely, the *trr file). What could I do?
> Regards
> Williams
> --
> 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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[gmx-users] Hydrophobic interaction analysis

[Nikhil Maroli]

Dear all,

is there any option in gromacs to study the hydrophobic interaction between
the two molecule over the simulation time !
-- 
Ragards,
Nikhil Maroli
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Re: [gmx-users] GROMACS 2016-beta1 released

[Nikhil Maroli]

really nice to hear,.

i will be getting GPU system with 3x GeForce GTX  980t,
happy to run new GROMACS,!

you all are simply great!!

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[gmx-users] GROMACS 2016-beta1 released

[Mark Abraham]

Hi GROMACS users,

The first beta release of GROMACS 2016 is available! We are making this
available to you to get an early taste of how GROMACS 2016 will look and
work, and most importantly to get feedback from you about how well things
work. While we try our hardest to keep the quality of GROMACS as high as
possible, we’re human, we overlook things while doing other things, and we
need your many pairs of eyes to help build a tool that we can all use to do
good science! We really need you to test your kinds of simulation on your
hardware, both for correctness and performance. This is particularly
important if you are using "interesting" hardware or compilers, because we
can't test all of them!

Please do not use this version for doing science you plan to publish - it
needs more testing before it’s reliable enough for that. Similarly, please
don’t use this version as a base for a project that bundles or forks GROMACS
.

What new things can you expect? (See the release notes for more details.)
* the version numbering has changed to be the year of the release, plus (in
future) a patch number. GROMACS 2016 will be the initial release from this
branch, then GROMACS 2016.1 will have the set of bugs that have been fixed
in GROMACS 2016, etc.
* various improvements to simulation performance, largely through our new
SIMD portability layer permitting us to accelerate various minor kernels,
but also improved use of multi-threading
* SIMD acceleration for POWER8 and ARM64
* enhancements to the pull code

Just so you know, a fair bit of the work done since 5.1 has been
re-organizational, rather than new features or faster performance. The SIMD
support for new kernels has let us run faster across the board with
moderate effort, but many of the payoffs are yet to come...

There’s lots of other new things, and old things removed - please see the
link to the release notes. All the content of GROMACS 5.1.2 (plus several
yet-to-be-released bug fixes) is present, apart from features that have
been removed.

If all goes to plan, we hope to ship the final 2016 release in June, but
that relies on people joining in and helping us test! We hope you will
consider making that contribution, so that we can continue to deliver
high-quality free simulation software that will be useful to you on day 1.

You can find the code, manual, release notes, installation instructions and
testsuite at the links below.

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2016-beta1.tar.gz
Documentation: http://manual.gromacs.org/documentation/2016-beta1/index.html
(includes install guide, user guide, reference manual)
Release Notes:
http://manual.gromacs.org/documentation/2016-beta1/ReleaseNotes/index.html
Test Suite:
http://gerrit.gromacs.org/download/regressiontests-2016-beta1.tar.gz

Happy testing!
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Re: [gmx-users] on atomtypes

[Justin Lemkul]

On 5/12/16 11:42 AM, Brett wrote:

Dear Justin,

You see, the ligand.itp contains the HS14 information as following,



  34NT1 ADP N67   -0.859  14.0067
   35  HS141 ADPH1070.406   1.0080

   36  HS141 ADPH1170.419   1.0080



But when I run
gmx grompp -f ions.mdp -c target_solv.gro -p topol.top -o ions.tpr,

it told me the "Atomtype HS14 not found".

Will you please show me the way to have the issue settled?



How did you generate the topology?  It's using an atom type that is not present 
in the parent force field, therefore you get an error.  Normally, external 
(non-GROMACS) sources of topologies will provide an augmented topology file that 
has the new [atomtypes] in it.  If not, then whatever you're doing is 
incompatible with the parent force field you're trying to use.


-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] on atomtypes

[Brett]

Dear Justin,

You see, the ligand.itp contains the HS14 information as following,



  34NT1 ADP N67   -0.859  14.0067
   35  HS141 ADPH1070.406   1.0080

   36  HS141 ADPH1170.419   1.0080



But when I run
gmx grompp -f ions.mdp -c target_solv.gro -p topol.top -o ions.tpr,

it told me the "Atomtype HS14 not found".

Will you please show me the way to have the issue settled?

Brett










At 2016-05-12 23:20:14, "Justin Lemkul"  wrote:
>
>
>On 5/12/16 11:17 AM, Brett wrote:
>> Dear All,
>>
>> Following is the part of the atomtypes.atp  for gromos54a7:
>>
>> O  15.99940 ; carbonyl oxygen (C=O)
>>OM  15.99940 ; carboxyl oxygen (CO-)
>>OA  15.99940 ; hydroxyl, sugar or ester oxygen
>>OE  15.99940 ; ether or ester oxygen
>>OW  15.99940 ; water oxygen
>> N  14.00670 ; peptide nitrogen (N or NH)
>>NT  14.00670 ; terminal nitrogen (NH2)
>>NL  14.00670 ; terminal nitrogen (NH3)
>>NR  14.00670 ; aromatic nitrogen
>>NZ  14.00670 ; Arg NH (NH2)
>>NE  14.00670 ; Arg NE (NH)
>> C  12.01100 ; bare carbon
>>   CH0  12.0110  ; bare sp3 carbon, 4 bound heavy atoms
>>   CH1  13.01900 ; aliphatic or sugar CH-group
>>   CH2  14.02700 ; aliphatic or sugar CH2-group
>>   CH3  15.03500 ; aliphatic CH3-group
>>   CH4  16.04300 ; methane
>>  CH2r  14.02700 ; CH2-group in a ring
>>   ...
>>
>> If I need to insert a new type list for example HS14 with weight 1.0080, 
>> should the word description of the atomtype (for example, "CH2-group in a 
>> ring" for "CH2r  14.02700") should be accurate or just a kind of reminder 
>> which the gromacas will not read?
>>
>
>It's a comment; it's not used for anything.  Note that atomtypes.atp is only 
>read by pdb2gmx, so if this is related to your earlier post (and if it is, 
>it's 
>better to continue a thread than to start a whole new topic) then you don't 
>need 
>to be editing this file.  You need to be adding parameters in ffnonbonded.itp 
>or 
>the ligand's .itp file itself.
>
>> In addition, the atomtypes.atp is a readonly file in 
>> /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/. WIll you please let me 
>> know how to save it after the HS14 atomtype was added?
>>
>
>Make a local copy of the directory, acquire admin privileges, or (most simply) 
>add missing parameters into the ligand's .itp file.
>
>-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] on atomtypes

[Justin Lemkul]

On 5/12/16 11:17 AM, Brett wrote:

Dear All,

Following is the part of the atomtypes.atp  for gromos54a7:

O  15.99940 ; carbonyl oxygen (C=O)
   OM  15.99940 ; carboxyl oxygen (CO-)
   OA  15.99940 ; hydroxyl, sugar or ester oxygen
   OE  15.99940 ; ether or ester oxygen
   OW  15.99940 ; water oxygen
N  14.00670 ; peptide nitrogen (N or NH)
   NT  14.00670 ; terminal nitrogen (NH2)
   NL  14.00670 ; terminal nitrogen (NH3)
   NR  14.00670 ; aromatic nitrogen
   NZ  14.00670 ; Arg NH (NH2)
   NE  14.00670 ; Arg NE (NH)
C  12.01100 ; bare carbon
  CH0  12.0110  ; bare sp3 carbon, 4 bound heavy atoms
  CH1  13.01900 ; aliphatic or sugar CH-group
  CH2  14.02700 ; aliphatic or sugar CH2-group
  CH3  15.03500 ; aliphatic CH3-group
  CH4  16.04300 ; methane
 CH2r  14.02700 ; CH2-group in a ring
  ...

If I need to insert a new type list for example HS14 with weight 1.0080, should the word 
description of the atomtype (for example, "CH2-group in a ring" for "CH2r  
14.02700") should be accurate or just a kind of reminder which the gromacas will not read?



It's a comment; it's not used for anything.  Note that atomtypes.atp is only 
read by pdb2gmx, so if this is related to your earlier post (and if it is, it's 
better to continue a thread than to start a whole new topic) then you don't need 
to be editing this file.  You need to be adding parameters in ffnonbonded.itp or 
the ligand's .itp file itself.



In addition, the atomtypes.atp is a readonly file in 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/. WIll you please let me 
know how to save it after the HS14 atomtype was added?



Make a local copy of the directory, acquire admin privileges, or (most simply) 
add missing parameters into the ligand's .itp file.


-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
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[gmx-users] on atomtypes

[Brett]

Dear All,

Following is the part of the atomtypes.atp  for gromos54a7:

O  15.99940 ; carbonyl oxygen (C=O)
   OM  15.99940 ; carboxyl oxygen (CO-)
   OA  15.99940 ; hydroxyl, sugar or ester oxygen
   OE  15.99940 ; ether or ester oxygen
   OW  15.99940 ; water oxygen
N  14.00670 ; peptide nitrogen (N or NH)
   NT  14.00670 ; terminal nitrogen (NH2)
   NL  14.00670 ; terminal nitrogen (NH3)
   NR  14.00670 ; aromatic nitrogen
   NZ  14.00670 ; Arg NH (NH2)
   NE  14.00670 ; Arg NE (NH)
C  12.01100 ; bare carbon
  CH0  12.0110  ; bare sp3 carbon, 4 bound heavy atoms
  CH1  13.01900 ; aliphatic or sugar CH-group
  CH2  14.02700 ; aliphatic or sugar CH2-group
  CH3  15.03500 ; aliphatic CH3-group
  CH4  16.04300 ; methane
 CH2r  14.02700 ; CH2-group in a ring
  ...

If I need to insert a new type list for example HS14 with weight 1.0080, should 
the word description of the atomtype (for example, "CH2-group in a ring" for 
"CH2r  14.02700") should be accurate or just a kind of reminder which the 
gromacas will not read?

In addition, the atomtypes.atp is a readonly file in 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/. WIll you please let me 
know how to save it after the HS14 atomtype was added?

Brett

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[gmx-users] Generating topology for a HEM protein with CHARMM27

[zeineb SI CHAIB]

Dear gmx users, 

I'm working on simulating a homodimer with its cofactors (hem, THG) and its 
substrate with GROMACS. 

Since my system is complex, I decided to start first with a monomere taking 
only protein residues and the hem group. 

When I run pdb2gmx, using CHARMM27 FF, I had this error: 
"Fatal error: There were 30 missing atoms in molecule Other_chain_A, if you 
want to use this incomplete topology anyhow, use the option -missing"! 

I think that this error is about hydrogen atoms but since my PDB is generated 
by X-RAY diffraction there is no hydrogen! What should I so? 

Thank you in advance for your help.

Zineb. 



  
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[gmx-users] Generating topology for a heme protein

[zeineb SI CHAIB]

Dear gmx users, 



I'm working on simulating a  homodimer with two cofactors (hem and 
tetrahydrofolat) and its substrate.

My system is complex so I decided to build my topology file step by step; 
starting with the protein and the heme (and see if it works). I run pdb2gmx, 
with CHARMM 27 FF on it and I had this error "Fatal error: There were 30 
missing atoms in molecule Other_chain_A2, if you want to use this incomplete 
topology anyhow, use the option -missing". 

I don't know what is ' Other_chain_A2'? my PDB file contain 1 chain: chain A; 
ATOM lines with protein residues and HETATM lines for HEM!!

How should I proceed in my case? Any tutorials. 

Thank you in advance for your help. 

Regards. 


Zeineb 





  
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[gmx-users] OpenMP

[ingram]

Dear Grommacs users,

I am trying to run some REMD calculations. I did not compile GROMACS 
with openMP, so when these calculations fail the first error I get is 
this:


Number of logical cores detected (12) does not match the number 
reported by OpenMP (3).

Consider setting the launch configuration manually!

And I dont understand why OpenMP is even being used by GROMACS.

THank you for your help

Teresa

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Re: [gmx-users] choosing box type

[Justin Lemkul]

On 5/12/16 5:57 AM, Upasana Ray wrote:

Dear User,
Can any one help me, what box type to choose for a protein so that it donot
comes out of the box



There is no "outside" of a periodic system and there is no box type that somehow 
magically prevents it.


-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] choosing box type

[Upasana Ray]

Dear User,
Can any one help me, what box type to choose for a protein so that it donot
comes out of the box
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Re: [gmx-users] on HS14 atomtype

[Sarath Chandra]

HS14 is not a standard atom type of the gromos 54a7 forcefield and so the
grompp is complaining about it.

You can have a look at this tutorial to get an idea on how to incorporate
non-standard molecules parameters into gromacs
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html

Regards,

Sarath


-- 


On 12 May 2016 at 13:06, Brett  wrote:

> Dear Sarah,
>
>
>
> I use the command grompp, it seems it can recognize all the other
> atomtypes in the ligand.itp.
>
>
> Thus how to solve the special HS14?
>
>
> Brett
>
>
>
>
>
>
>
>
>
> At 2016-05-12 15:03:59, "Sarath Chandra" 
> wrote:
> >What command did you use (pdb2gmx/grompp)? You have to check whether your
> >ligand.itp is referenced in your topol.top for grompp to find the
> atomtypes
> >present in your gro.
> >
> >Regards,
> >
> >Sarath
> >
> >--
> >Sarath Chandra Dantu, PhD, ELS
> >Room No. 606, New BSBE Building
> >Department of Biosciences and Bioengineering
> >Indian Institute of Technology Bombay
> >Powai Mumbai, 400-076, India
> >
> >
> >On 12 May 2016 at 11:40, Brett  wrote:
> >
> >> Dear All,
> >>
> >> By ADP with 54a7 force field, I got a ligand.itp, which contains
> atomtype
> >> HS14. However when I run the md by gromacs with that ligand.itp, it
> told me
> >> the "Atomtype HS14 not found".
> >>
> >> WIll you please tell me how to make gromacs recognize the atomtype HS14?
> >>
> >> Brett
> >> --
> >> 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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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
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Re: [gmx-users] problem to continue MD run

[Mark Abraham]

Hi,

Please report the commands you are running, and copy and paste the error
message. Otherwise we're just wasting time guessing :-)

Mark

On Thu, May 12, 2016 at 4:12 AM Williams Miranda <
williams.mira...@ucalgary.ca> wrote:

> Dear GROMACS users
> I need to continue an unfinished simulation. Because of disk space, I
> deleted the *trr file. Unfortunately, when I try to continue the run using
> the -cpi option, gromacs complains that 1 of 4 files needed to continue the
> run is missing (likely, the *trr file). What could I do?
> Regards
> Williams
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Re: [gmx-users] how to order gpus on different nodes

[Mark Abraham]

Hi,

On Thu, May 12, 2016 at 8:28 AM Ming Tang  wrote:

> Dear experts,
>
> I can order 2 gpus on one node from HPC using the following script:
>
> #PBS -l select=1:ncpus=2:ngpus=2:mpiprocs=2:mem=2gb
>
> mpiexec_mpt -n 2 gmx_mpi mdrun -v -deffnm npt -nb gpu -gpu_id 01 -ntomp 2
>
> however when I used the following script to order 4 gpus on 2 nodes, it
> gave me an error saying gpu cannot be detected.
>

Please copy and paste the actual error message. Details are important for
computer-related problems.

#PBS -l select=2:ncpus=2:ngpus=2:mpiprocs=2:mem=4gb
>
>
> mpiexec_mpt -n 4 gmx_mpi mdrun -cpi -cpo -c relax.pdb -nb gpu -gpu_id 0011
> -ntomp4
>
> Does anybody know how to order gpus on different nodes?
>

See
http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html#examples-for-mdrun-on-more-than-one-node,
and note that -gpu_id indexes GPUs on each node, so probably you want
-gpu_id 01 for the mapping from the two ranks on each node to the two GPUs
on each node.

Mark


> Thank you.
>
>
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Re: [gmx-users] GPUs performance on Gromacs calculation

[Mark Abraham]

Hi,

On Thu, May 12, 2016 at 8:26 AM Ming Tang  wrote:

> Dear experts,
>
> I did SMD on 2 M2090 GPUs and 16 CPUs on one node. The simulation ran
> around 500 steps every 15 minutes.
> However, the SMD simulation ran around 68000 steps using 96 CPUs without
> GPU.
> Is this because the M2090 GPU type works badly on Gromacs?
>

We can't possibly tell what's going on - you've reported a rate and a total
number of steps for two different runs :-) If you want some feedback then
we need to know things like GROMACS version, what you are simulating, and
for you to share some .log files on a file-sharing service. The list does
not accept attachments


> Our Uni has the following types of GPU. Could anybody help to tell me
> which one is better for my SMD simulation?
>
> * 4 x M2050 Nvidia Tesla GPUs
> * 8 x M2090 Nvidia Tesla GPUs (2 per node)
> * 12 x K40 Nvidia Tesla GPUs (2 per node)
> * 8 x Intel Xeon Phi 5110P Co-processors (2 per node)
> * 1 x Bitware S5-PCIe-HQ with Altera Stratix V FPGA
>

The Teslas are probably all fine, the Phis probably useful only for
reaction-field simulations, and the FPGA useless.

Mark


> Thank you.
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Re: [gmx-users] on HS14 atomtype

[Sarath Chandra]

What command did you use (pdb2gmx/grompp)? You have to check whether your
ligand.itp is referenced in your topol.top for grompp to find the atomtypes
present in your gro.

Regards,

Sarath

-- 
Sarath Chandra Dantu, PhD, ELS
Room No. 606, New BSBE Building
Department of Biosciences and Bioengineering
Indian Institute of Technology Bombay
Powai Mumbai, 400-076, India


On 12 May 2016 at 11:40, Brett  wrote:

> Dear All,
>
> By ADP with 54a7 force field, I got a ligand.itp, which contains atomtype
> HS14. However when I run the md by gromacs with that ligand.itp, it told me
> the "Atomtype HS14 not found".
>
> WIll you please tell me how to make gromacs recognize the atomtype HS14?
>
> Brett
> --
> Gromacs Users mailing list
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[gmx-users] how to order gpus on different nodes

[Ming Tang]

Dear experts,

I can order 2 gpus on one node from HPC using the following script:

#PBS -l select=1:ncpus=2:ngpus=2:mpiprocs=2:mem=2gb

mpiexec_mpt -n 2 gmx_mpi mdrun -v -deffnm npt -nb gpu -gpu_id 01 -ntomp 2

however when I used the following script to order 4 gpus on 2 nodes, it gave me 
an error saying gpu cannot be detected.

#PBS -l select=2:ncpus=2:ngpus=2:mpiprocs=2:mem=4gb


mpiexec_mpt -n 4 gmx_mpi mdrun -cpi -cpo -c relax.pdb -nb gpu -gpu_id 0011 
-ntomp4

Does anybody know how to order gpus on different nodes?

Thank you.


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[gmx-users] on HS14 atomtype

[Brett]

Dear All,

By ADP with 54a7 force field, I got a ligand.itp, which contains atomtype HS14. 
However when I run the md by gromacs with that ligand.itp, it told me the 
"Atomtype HS14 not found".

WIll you please tell me how to make gromacs recognize the atomtype HS14?

Brett
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[gmx-users] GPUs performance on Gromacs calculation

[Ming Tang]

Dear experts,

I did SMD on 2 M2090 GPUs and 16 CPUs on one node. The simulation ran around 
500 steps every 15 minutes.
However, the SMD simulation ran around 68000 steps using 96 CPUs without GPU.
Is this because the M2090 GPU type works badly on Gromacs?

Our Uni has the following types of GPU. Could anybody help to tell me which one 
is better for my SMD simulation?

* 4 x M2050 Nvidia Tesla GPUs
* 8 x M2090 Nvidia Tesla GPUs (2 per node)
* 12 x K40 Nvidia Tesla GPUs (2 per node)
* 8 x Intel Xeon Phi 5110P Co-processors (2 per node)
* 1 x Bitware S5-PCIe-HQ with Altera Stratix V FPGA

Thank you.
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