date:20140709

Re: [gmx-users] Regarding gmx gangle selection

2014-07-09 Thread Venkat Reddy

Hi,
Apologies for the minor mistake in typing. Actually the argument in group1
should be 'Resname RES and name B A'. Sorry for the confusion.

On Wed, Jul 9, 2014 at 12:19 PM, Venkat Reddy  wrote:

> Dear all,
> I am trying to analyse my lipid vesicle system using gromacs-5.0. I am
> using gmx gangle to find the angle between lipid tails. In the gmx gangle
> help section, its mentioned that "For vectors, the selected positions set
> the endpoints of the vector". But nothing is mentioned about direction of
> vector. For example, if I select  'Resname RES and name A B' to denote my
> vector; The direction of the vector is from A to B. Please correct me if I
> am wrong.
>
> If I want to calculate the angle ABC in a residue RES, -group1 'Resname
> RES and name A B' -group2 'Resname RES and name B C', is this a valid
> selection?
>
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
>

-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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[gmx-users] polarizable water and non-polarizable alkanes

2014-07-09 Thread Yana Tsoneva

Dear colleagues,

I am running simulations using Gromacs - 4.6.5 and my systems consist of 
water/different oils. Until now I have used TIP4P water model and amber99 
for the alkanes.

I need to run the same simulations, but with a polarizable water model. I 
succeeded in simulating pure polarizable water (sw-rigid of van Gusteren), 
but now I have problems adding the alkanes. I know that I should not mix 
different force fields, but is there any chance for me to simulate 
polarizable water and non-polarizable alkanes? If there is one, can you tell 
me how to do it? I read that there is a modification of the CHARMM force 
field to simulate alkanes with Drude oscillators. Is this the way to achieve 
compatibility of the force fields?

Thanks in advance,
Yana
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[gmx-users] parameters for Ag+ ions

2014-07-09 Thread Rebeca García Fandiño

Hello,
I need to simulate an organic dimer complexed with Ag+ with GROMACS. For the 
organic molecule I am using GAFF, so I would like to find Ag+ parameters in 
Amber or GAFF. Could anyone help me to find them?
Some time ago I have worked with Ag clusters, and I have found appropiate sigma 
and epsilon values for Ag (0). I suppose that these sigma and epsilon values 
cannot be used for Ag+, is it OK?  Sigma and epsilon are related with the 
radius of the element, so I suppose that it should change from Ag(0) to Ag+. 
Any comment will be appreciated.
Best wishes,
Rebeca.
  
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Re: [gmx-users] GPU tutorial

2014-07-09 Thread Chandan Choudhury

Dear Raman,
1. For using GPU enabled gromacs, the gromacs must be installed using
-DGMX_GPU=ON
flag.
2. The commands are all same as with the non gpu enabled ones. For running
the mdrun program, you need to incorporate
cutff-scheme = verlet in the mdp file (Details can be viewed at
http://www.gromacs.org/Documentation/Cut-off_schemes). Verlet cutoff scheme is
the default for the 5.0 version of gmx).

Hope this helps.

Chandan


On Wed, Jul 9, 2014 at 9:47 AM, Raman Parkesh  wrote:

> Hi,
> I am new to Gromacs GPU. I was wondering if anyone know about the gpu
> related gromacs tutorial particularly about the input files for running
> gpu
> enabled MD simulations.
>
> Regards,
> Raman
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-- 

--
Chandan Kumar Choudhury
National Chemical Laboratory, Pune
India
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[gmx-users] Reducing the dimensionality of my cross correlation matrix

2014-07-09 Thread Bailey A.

Dear gromacs users,

I posted a similar question the other day, but it was probably too long, so 
here it is more concisely:

I've taken the ascii output of g_covar and built the 3N x 3N covariance matrix 
in MATLAB from the 3N^2 x 3 matrix, which I've then normalized to get a 3N x 3N 
cross correlation matrix.

What I'd like is a N x N matrix, and so I've added together the three N x N 
parts of the 3N x 3N matrix and divided by 3 to get my N x N matrix.

However this doesn't look the same as something I'd previously calculated using 
Ran Friedman's amended g_covar script and I'm trying to understand the 
discrepancy.

Can anyone advise me on what the dimension reduction step should be? I can post 
my code if that helps.

Many thanks,

Alistair


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[gmx-users] Problem with g_chi options

2014-07-09 Thread Anna Stopka


Hi everybody,

I wrote last week, but nobody answered. So I write again, still having the same 
problem:

I want do an analysis of my simulation with the tool g_chi.
The problem is, that the optional output options don't work.

I use the following command:

g_chi -s config.gro -f traj.xtc -oh -all

and all I get are the standard output files chi.log and order.xvg.
I am not sure if it has something to do with the following warning I get:

WARNING: not all dihedrals found in topology (only 1056 out of 1746)!

Honestly, I don't understand why I get this warning, because all the
input files are fine.

Thanks for your help!
Best regards,
Anna


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Re: [gmx-users] GPU tutorial

2014-07-09 Thread Raman Parkesh

Thanks Amin and Chandan for these helpful tips. I have now successfully
installed GPU enabled Gromacs. Hope to have some fun in running faster
simulations.

Regards,
Raman


On 9 July 2014 15:07, Chandan Choudhury  wrote:

> Dear Raman,
> 1. For using GPU enabled gromacs, the gromacs must be installed using
> -DGMX_GPU=ON
> flag.
> 2. The commands are all same as with the non gpu enabled ones. For running
> the mdrun program, you need to incorporate
> cutff-scheme = verlet in the mdp file (Details can be viewed at
> http://www.gromacs.org/Documentation/Cut-off_schemes). Verlet cutoff
> scheme is
> the default for the 5.0 version of gmx).
>
> Hope this helps.
>
> Chandan
>
>
> On Wed, Jul 9, 2014 at 9:47 AM, Raman Parkesh  wrote:
>
> > Hi,
> > I am new to Gromacs GPU. I was wondering if anyone know about the gpu
> > related gromacs tutorial particularly about the input files for running
> > gpu
> > enabled MD simulations.
> >
> > Regards,
> > Raman
> > --
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> > posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
>
> --
> Chandan Kumar Choudhury
> National Chemical Laboratory, Pune
> India
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Re: [gmx-users] Problems in compiling GROMACS with VMD plugin (Roland Schulz)

2014-07-09 Thread ming ma

Hi Roland

Now I know how to reply more specifically. Here is the email I sent
yesterday :)

Thanks for your reply.

>> GMX_USE_PLUGINS has to be enabled in your CMackeCache.txt. Are you
building
>> under Linux? It probably didn't find dlopen support. Look for "Result of
>> test for dlopen" when you run cmake in a new build folder. You can see in
>> CMakeFiles/CMakeError.log why the dlopen test fails.

First, I need to apologize as I don't know how to reply to the contents
related to my questions only (my thread), so I just replied here directly.

First question, how can I enabled GMX_USE_PLUGINS? Intuitively, I edit the
file in gromacs-xxx/build/CMakeCache.txt manually by
setting GMX_USE_PLUGINS fro m OFF to ON.

However, it doesn't work. I first grep PLUGINS in CMakeCache.txt, and got
the following results

[ming@mingtlv myserial]$ grep PLUGINS CMakeCache.txt
GMX_LOAD_PLUGINS:BOOL=ON
//ADVANCED property for variable: GMX_LOAD_PLUGINS
GMX_LOAD_PLUGINS-ADVANCED:INTERNAL=1
GMX_USE_PLUGINS:INTERNAL=OFF


>From the last line, it seems that GROMACS didn't build with PLUGINS, though
the first one is ON.

Then I grepped dlopen, DLOPEN, vmd, VMD, PLUGINS, plugins in both
CMakeFiles/CMakeError.log and found nothing.

In the output of cmake, I found the following things for dlopen, DLOPEN and
vmd.

[ming@mingtlv gromacs-4.6.5]$ grep dlopen s.log
-- Checking for dlopen
-- Checking for dlopen - found
[  3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmddlopen.c.o

[ming@mingtlv gromacs-4.6.5]$ grep DLOPEN s.log
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success

[ming@mingtlv gromacs-4.6.5]$ grep vmd s.log
[  3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmddlopen.c.o
[  6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmdio.c.o

So, I still have no idea what's the problem Any suggestions?

Best
Ming


2014-07-08 21:34 GMT+03:00 <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se>:

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> Today's Topics:
>
>1. Re: gmx-5.0 features (Szil?rd P?ll)
>2. Re: gmx-5.0 features (Szil?rd P?ll)
>3. Re: hardware setup for gmx (Szil?rd P?ll)
>4. Re: hardware setup for gmx (Szil?rd P?ll)
>5. Re: strange but true : How to explain and avoid? (Justin Lemkul)
>6. Re: Problems in compiling GROMACS with VMD plugin (Roland Schulz)
>
>
> --
>
> Message: 1
> Date: Tue, 8 Jul 2014 19:25:42 +0200
> From: Szil?rd P?ll 
> To: gmx-us...@gromacs.org, Michael Brunsteiner 
> Cc: "gromacs.org_gmx-users@maillist.sys.kth.se"
> 
> Subject: Re: [gmx-users] gmx-5.0 features
> Message-ID:
>  egxq8...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Thu, Jul 3, 2014 at 4:05 PM, Michael Brunsteiner 
> wrote:
>
> >
> >
> > Hi,
> >
> > I am sorry in case I overlooked the answers in the release-notes,
> > but I didn't find there answers to:
> > 1) does gmx-5.0 support free energy calculations + GPU ?
> >
>
> Yes.
>
>
> >
> > 2) does gmx-5.0 support double precision + GPU ?
> >
>
> No.
>
> Cheers,
> --
> Szil?rd
>
>
> >
> > cheers
> > michael
> >
> > ===
> >
> >
> > Why be happy when you could be normal?
> > --
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> >
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> > posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> P?ll Szil?rd
>
>
> --
>
> Message: 2
> Date: Tue, 8 Jul 2014 19:25:42 +0200
> From: Szil?rd P?ll 
> To: gmx-us...@gromacs.org, Michael Brunsteiner 
> Cc: "gromacs.org_gmx-users@maillist.sys.kth.se"
> 
> Subject: Re: [gmx-users] gmx-5.0 features
> Message-ID:
>  egxq8...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Thu, Jul 3, 2014 at 4:05 PM, Michael Brunsteiner 
> wrote:
>
> >
> >
> > Hi,
> >
> > I am sorry in case I overlooked the answers in the release-notes,
> > but I didn't find there answers to:
> > 1) does gmx-5.0 support free energy calculations + GPU ?
> >
>
> Yes.
>
>
> >
> > 2) does gmx-5.0 support double precision + GPU ?
> >
>
> No.
>
> Cheers,
> --
> Szil?rd
>
>
> >
> > cheers
> > michael
>

[gmx-users] Error in system_inflate.gro coordinates does not match

2014-07-09 Thread RINU KHATTRI

hello every one
I am working on complex with popc membrane i did

perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat

after this step minimization

grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr

i got error
Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 10224)
 does not match topology (topol.top, 10245)
i have been removed 6 lipid molecules in my topology file according to
output i got one thing new in my system_inflate.gro file the written
displayed atom is 10224 but after counting it is 10536 so if i correct it
difference is more
in topology file [molecule]
protein chain 1
UNK1
POPC 122
how to resolve  it
kindly help
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Re: [gmx-users] Regarding gmx gangle selection

2014-07-09 Thread Teemu Murtola

The vector is from the first position to the second, from the third to the
fourth and so on. But the order of parameters for, e.g., "name", does not
affect the order of positions (see earlier discussion on the list): the
atoms are always selected in the order of increasing atom indices. If you
want to reverse the vector, you can use "permute 2 1" at the end of the
selection.
On Jul 9, 2014 10:03 AM, "Venkat Reddy"  wrote:

> Hi,
> Apologies for the minor mistake in typing. Actually the argument in group1
> should be 'Resname RES and name B A'. Sorry for the confusion.
>
>
> On Wed, Jul 9, 2014 at 12:19 PM, Venkat Reddy  wrote:
>
> > Dear all,
> > I am trying to analyse my lipid vesicle system using gromacs-5.0. I am
> > using gmx gangle to find the angle between lipid tails. In the gmx gangle
> > help section, its mentioned that "For vectors, the selected positions set
> > the endpoints of the vector". But nothing is mentioned about direction of
> > vector. For example, if I select  'Resname RES and name A B' to denote my
> > vector; The direction of the vector is from A to B. Please correct me if
> I
> > am wrong.
> >
> > If I want to calculate the angle ABC in a residue RES, -group1 'Resname
> > RES and name A B' -group2 'Resname RES and name B C', is this a valid
> > selection?
> >
> > --
> > With Best Wishes
> > Venkat Reddy Chirasani
> > PhD student
> > Laboratory of Computational Biophysics
> > Department of Biotechnology
> > IIT Madras
> > Chennai
> > INDIA-600036
> >
>
>
>
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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Re: [gmx-users] polarizable water and non-polarizable alkanes

2014-07-09 Thread Justin Lemkul




On 7/9/14, 3:56 AM, Yana Tsoneva wrote:

Dear colleagues,

I am running simulations using Gromacs - 4.6.5 and my systems consist of
water/different oils. Until now I have used TIP4P water model and amber99
for the alkanes.

I need to run the same simulations, but with a polarizable water model. I
succeeded in simulating pure polarizable water (sw-rigid of van Gusteren),
but now I have problems adding the alkanes. I know that I should not mix
different force fields, but is there any chance for me to simulate
polarizable water and non-polarizable alkanes? If there is one, can you tell
me how to do it? I read that there is a modification of the CHARMM force
field to simulate alkanes with Drude oscillators. Is this the way to achieve
compatibility of the force fields?



The CHARMM Drude FF for alkanes was parametrized against SWM4-DP, not SW, so 
such a combination is not valid.  You need a self-consistent force field.  I 
doubt that an additive model of alkanes in conjunction with a polarizable model 
of water would be reliable.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] Error in system_inflate.gro coordinates does not match

2014-07-09 Thread Justin Lemkul




On 7/9/14, 6:17 AM, RINU KHATTRI wrote:

hello every one
I am working on complex with popc membrane i did

perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat

after this step minimization

grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr

i got error
Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 10224)
  does not match topology (topol.top, 10245)
i have been removed 6 lipid molecules in my topology file according to
output i got one thing new in my system_inflate.gro file the written
displayed atom is 10224 but after counting it is 10536 so if i correct it
difference is more


I don't know what this means, but the number of atoms that grompp is finding is 
going to be correct.



in topology file [molecule]
protein chain 1
UNK1
POPC 122
how to resolve  it


I would venture a guess that UNK has 21 atoms.  I don't know that InflateGRO 
handles arbitrary molecules, so it may have gotten deleted upon inflation. 
Check system_inflated.gro; it will be very obvious if it is missing.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] Regarding gmx gangle selection

2014-07-09 Thread Venkat Reddy

Thank you Sir for the clarification.


On Wed, Jul 9, 2014 at 3:57 PM, Teemu Murtola 
wrote:

> The vector is from the first position to the second, from the third to the
> fourth and so on. But the order of parameters for, e.g., "name", does not
> affect the order of positions (see earlier discussion on the list): the
> atoms are always selected in the order of increasing atom indices. If you
> want to reverse the vector, you can use "permute 2 1" at the end of the
> selection.
> On Jul 9, 2014 10:03 AM, "Venkat Reddy"  wrote:
>
> > Hi,
> > Apologies for the minor mistake in typing. Actually the argument in
> group1
> > should be 'Resname RES and name B A'. Sorry for the confusion.
> >
> >
> > On Wed, Jul 9, 2014 at 12:19 PM, Venkat Reddy 
> wrote:
> >
> > > Dear all,
> > > I am trying to analyse my lipid vesicle system using gromacs-5.0. I am
> > > using gmx gangle to find the angle between lipid tails. In the gmx
> gangle
> > > help section, its mentioned that "For vectors, the selected positions
> set
> > > the endpoints of the vector". But nothing is mentioned about direction
> of
> > > vector. For example, if I select  'Resname RES and name A B' to denote
> my
> > > vector; The direction of the vector is from A to B. Please correct me
> if
> > I
> > > am wrong.
> > >
> > > If I want to calculate the angle ABC in a residue RES, -group1 'Resname
> > > RES and name A B' -group2 'Resname RES and name B C', is this a valid
> > > selection?
> > >
> > > --
> > > With Best Wishes
> > > Venkat Reddy Chirasani
> > > PhD student
> > > Laboratory of Computational Biophysics
> > > Department of Biotechnology
> > > IIT Madras
> > > Chennai
> > > INDIA-600036
> > >
> >
> >
> >
> > --
> > With Best Wishes
> > Venkat Reddy Chirasani
> > PhD student
> > Laboratory of Computational Biophysics
> > Department of Biotechnology
> > IIT Madras
> > Chennai
> > INDIA-600036
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
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> > posting!
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters

2014-07-09 Thread Nikolaos Michelarakis

Hello again,

This what I have been trying to do so far. This is the command to run the
script:

./cgenff_charmm2gmx.py PTC 2e7z-ptc.mol2 2e7z-ptc.str charmm36-mar2014.ff

and this is the error I have been getting along with 2 Notes:

NOTE2: Please be sure to use the same version of CGenFF in your simulations
that was used during parameter generation:
--Version of CGenFF detected in  charmm36-mar2014.ff/forcefield.doc : 2b8

NOTE3: In order to avoid duplicated parameters, do NOT select the 'Include
parameters that are already in CGenFF' option when uploading a molecule
into CGenFF.

error in atomgroup.py: read_mol2_coor_only: natoms in mol2 .ne. top
96 142


The file names I am using are:
 2e7z-ptc.str  charmm36-mar2014.ff
2e7z-ptc.mol2  cgenff_charmm2gmx.py

These are the contents of the .mol2 and .str files respectively:

https://drive.google.com/file/d/0BzqRbRx4Ynf0TUg3blBOTmV0Qzg/edit?usp=sharing
(mol2)

https://drive.google.com/file/d/0BzqRbRx4Ynf0VThMSnNYMU1XVmM/edit?usp=sharing
(str)

Thanks a lot,

Nicholas
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Re: [gmx-users] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters

2014-07-09 Thread Justin Lemkul




On 7/9/14, 8:11 AM, Nikolaos Michelarakis wrote:

Hello again,

This what I have been trying to do so far. This is the command to run the
script:

./cgenff_charmm2gmx.py PTC 2e7z-ptc.mol2 2e7z-ptc.str charmm36-mar2014.ff

and this is the error I have been getting along with 2 Notes:

NOTE2: Please be sure to use the same version of CGenFF in your simulations
that was used during parameter generation:
--Version of CGenFF detected in  charmm36-mar2014.ff/forcefield.doc : 2b8

NOTE3: In order to avoid duplicated parameters, do NOT select the 'Include
parameters that are already in CGenFF' option when uploading a molecule
into CGenFF.

error in atomgroup.py: read_mol2_coor_only: natoms in mol2 .ne. top
96 142


The file names I am using are:
  2e7z-ptc.str  charmm36-mar2014.ff
2e7z-ptc.mol2  cgenff_charmm2gmx.py

These are the contents of the .mol2 and .str files respectively:

https://drive.google.com/file/d/0BzqRbRx4Ynf0TUg3blBOTmV0Qzg/edit?usp=sharing
(mol2)

https://drive.google.com/file/d/0BzqRbRx4Ynf0VThMSnNYMU1XVmM/edit?usp=sharing
(str)



There's a mismatch between the structures.  Your coordinates (mol2) have 96 
atoms, but the topology has 142.  The problem comes from the fact that your mol2 
file has no H atoms.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] 1 gpu vs 2 gpu speedup

2014-07-09 Thread Harry Mark Greenblatt

BS"D

Dear Szilárd,

Thanks very much for your reply.


This compiler is very outdated, you should use at least gcc 4.7 or 4.8
for best performance - especially the CPU-only runs should get quite a
bit faster.

Thanks, point taken.  The person who compiled this on the test machine just 
used what RedHat 6.5 had to offer.


Setup Wall Time (s) ns/day speedup (relative to 1st result)

6 cores, no gpu 12,996 6.65
12 cores, no gpu 7037 12.3 1.85
6 cores, 1 gpu 1853 46.6 7.01
2 x 6 cores, 2 gpu 1342 64.4 9.68

Is that really 7x speedup wrt 6 cores? That should be more like 3-4x,
so I suspect your CPU-only performance is 1.5-2x off.

The speedup would be relative to the CPU.  This is a Sandy Bridge CPU running 
at 2.3GHz, not an Ivy Bridge v2 model.  Perhaps you've gotten used to later 
CPU's.

The job certainly ran on 2 MPI ranks, using 12 cores and 2 GPU's (~75% usage 
each).  I'm wondering if I didn't specify the proper mdrun command line 
arguments (based on log file, see below, where it complains about too few total 
ranks), or perhaps my system is not amenable to efficient GPU acceleration 
beyond one GPU.

Comments?  Below is some of the last log file:
...
Number of hardware threads detected (12) does not match the number reported by 
OpenMP (6).

This does not look good, I think it means that your job scheduler is
expecting you to use 6 cores. You should make sure that thread
affinities are set correctly and getting rid of the above could help
too.


I suspect my mdrun arguments (or lack thereof) might be at fault.  I did try 
"-pin on" but it had no effect.


...

You may want to try using multiple ranks per GPU, e.g.
mpirun -np 4 mdrun -gpu_id 0011
mpirun -np 6 mdrun -gpu_id 000111


Ok, will see what happens.
Thanks very much

Harry


-

Harry M. Greenblatt

Associate Staff Scientist

Dept of Structural Biology

Weizmann Institute of SciencePhone:  972-8-934-3625

234 Herzl St.Facsimile:   972-8-934-4159

Rehovot, 76100

Israel


harry.greenbl...@weizmann.ac.il







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[gmx-users] Fwd: DSSP- error

2014-07-09 Thread Uma Devi

Dear gromacs users,
i am using gromacs 4.6.2. i tried the secondary structure analysis, using
do_dssp. but i got the following error.
Fatal error:
Failed to execute command: /usr/local/bin/dssp.exe -na ddFyZGQ1 ddTj0ABl >
/dev/null 2> /dev/null.

i am using amd, with cemtos. i downloaded dssp executable, then placed it
in /usr/local/bin.
i gave permission using chmod a+x dssp.
then i export dssp from my folder using
export DSSP=/usr/local/bin/dssp
please help me to sort it out the problem


Thanks in advances

Umadevi Palanivel
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[gmx-users] Passing group of solvent molecules by argument in genion

2014-07-09 Thread Marco Rougeth

Hello people,

is there any way of pass what group of solvent I want to use in *genion*?
I'm creating a non-interactive script that calls genion, any thoughts about
how I would solve it?

Thanks!
Marco.
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Re: [gmx-users] Graphene topology file

2014-07-09 Thread #SUKRITI GUPTA#

Thanks for the reply Justin. I just checked my box size again and found it to 
be smaller than the required. Hence I changed the size and ran the simulation 
again. This time energy minimization happened correctly without any change in 
the graphene structure. But when I am doing npt, the water is suddenly moving 
far away from the graphene sheet any tries to agglomerate together causing the 
box size to increase drastically. It is almost like the box is about to 
explode. Its size changes from 2.5A to 11A.

Can you please help me figure out the problem.

Thanks and Regards
Sukriti

Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | 
Nanyang Technological University
Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, 
Singapore(637459)
Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg

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

Sent: Tuesday, July 8, 2014 7:41 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Graphene topology file

On 7/8/14, 1:23 AM, #SUKRITI GUPTA# wrote:
> Hi Justin,
>
> Thanks a lot for your replies. I want to simulate a half cell with graphene
> electrode only on one side, hence i am using pbc in only xy direction i.e.
> direction of graphene sheet, so that I have a infinite size graphene sheet
> with no side effects. But if I use 3D pbc then graphene sheet effect will be
> there on the other side of the box also, which I don't want.
>
> Also if I use 3D PBC or 2D PBC, the major problem is that even after freezing
> graphene sheet, after doing energy minimization, the sheet remains linear but
> becomes distorted and new bonds are formed between terminal carbons. I don't
> know what is the problem with my system.
>

That sounds like a topology problem.  Using "periodic_molecules = yes" should
allow for bonding across periodic boundaries, so bonds shouldn't be recognized
between atoms at the "ends" of your sheet within the unit cell.  Is that what
you're describing?  Images would help.  Check the topology carefully to make
sure it has been constructed properly.  A correctly sized box with g_x2top -pbc
should create a sensible topology.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] 1 gpu vs 2 gpu speedup

2014-07-09 Thread Szilárd Páll

On Wed, Jul 9, 2014 at 2:27 PM, Harry Mark Greenblatt
 wrote:
> BS"D
>
> Dear Szilárd,
>
> Thanks very much for your reply.
>
>
> This compiler is very outdated, you should use at least gcc 4.7 or 4.8
> for best performance - especially the CPU-only runs should get quite a
> bit faster.
>
> Thanks, point taken.  The person who compiled this on the test machine just 
> used what RedHat 6.5 had to offer.
>
>
> Setup Wall Time (s) ns/day speedup (relative to 1st result)
>
> 6 cores, no gpu 12,996 6.65
> 12 cores, no gpu 7037 12.3 1.85
> 6 cores, 1 gpu 1853 46.6 7.01
> 2 x 6 cores, 2 gpu 1342 64.4 9.68
>
> Is that really 7x speedup wrt 6 cores? That should be more like 3-4x,
> so I suspect your CPU-only performance is 1.5-2x off.
>
> The speedup would be relative to the CPU.  This is a Sandy Bridge CPU running 
> at 2.3GHz, not an Ivy Bridge v2 model.  Perhaps you've gotten used to later 
> CPU's.

The Sandy Bridge-Ivy Bridge difference at identical clock speed is
quite small (<5%, I think). So your CPU-only performance is poor
(which I'm guessing based on the unusually high GPU speedup) probably
because of the old compiler.

> The job certainly ran on 2 MPI ranks, using 12 cores and 2 GPU's (~75% usage 
> each).  I'm wondering if I didn't specify the proper mdrun command line 
> arguments (based on log file, see below, where it complains about too few 
> total ranks), or perhaps my system is not amenable to efficient GPU 
> acceleration beyond one GPU.
>
> Comments?  Below is some of the last log file:
> ...
> Number of hardware threads detected (12) does not match the number reported 
> by OpenMP (6).
>
> This does not look good, I think it means that your job scheduler is
> expecting you to use 6 cores. You should make sure that thread
> affinities are set correctly and getting rid of the above could help
> too.
>
>
> I suspect my mdrun arguments (or lack thereof) might be at fault.  I did try 
> "-pin on" but it had no effect.

The mdrun arguments can't influence the CPU count the OpenMP library
reports, that's something typically environment variables control.

>
> ...
>
> You may want to try using multiple ranks per GPU, e.g.
> mpirun -np 4 mdrun -gpu_id 0011
> mpirun -np 6 mdrun -gpu_id 000111
>
>
> Ok, will see what happens.
> Thanks very much
>
> Harry
>
>
> -
>
> Harry M. Greenblatt
>
> Associate Staff Scientist
>
> Dept of Structural Biology
>
> Weizmann Institute of SciencePhone:  972-8-934-3625
>
> 234 Herzl St.Facsimile:   972-8-934-4159
>
> Rehovot, 76100
>
> Israel
>
>
> harry.greenbl...@weizmann.ac.il
>
>
>
>
>
>
>
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Re: [gmx-users] Reducing the dimensionality of my cross correlation matrix

2014-07-09 Thread Bailey A.

I answered my own question and solved this, just a typo in my code. If anyone 
else has the same issue, drop me a line.

I'll put a script up on MATLAB central at some point too.

Alistair 

-Original Message-
From: Bailey A. [mailto:ab...@soton.ac.uk] 
Sent: 09 July 2014 10:40
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Reducing the dimensionality of my cross correlation matrix

Dear gromacs users,

I posted a similar question the other day, but it was probably too long, so 
here it is more concisely:

I've taken the ascii output of g_covar and built the 3N x 3N covariance matrix 
in MATLAB from the 3N^2 x 3 matrix, which I've then normalized to get a 3N x 3N 
cross correlation matrix.

What I'd like is a N x N matrix, and so I've added together the three N x N 
parts of the 3N x 3N matrix and divided by 3 to get my N x N matrix.

However this doesn't look the same as something I'd previously calculated using 
Ran Friedman's amended g_covar script and I'm trying to understand the 
discrepancy.

Can anyone advise me on what the dimension reduction step should be? I can post 
my code if that helps.

Many thanks,

Alistair



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Re: [gmx-users] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters

2014-07-09 Thread Nikolaos Michelarakis

Hey,

Thanks a lot, I fixed the file but I am now getting a python error, I think.

Traceback (most recent call last):
  File "./cgenff_charmm2gmx.py", line 792, in 
m.read_mol2_coor_only(mol2_name)
  File "./cgenff_charmm2gmx.py", line 720, in read_mol2_coor_only
atomi = int(entry[0])-1
ValueError: invalid literal for int() with base 10: ''

something wrong with the coordinates?

the new mol2 file is:

https://drive.google.com/file/d/0BzqRbRx4Ynf0SV9rZnhhTmxGRmM/edit?usp=sharing

cheers!

Nicholas
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[gmx-users] Regarding 'insolidangle' and some tools

2014-07-09 Thread Venkat Reddy

Dear Teemu,

I have been following one of your presentations on "Improved Gromacs
analysis using dynamic selections" and also referring your publication on
LDL modeling and dynamics. My simulation system is quite similar to your
LDL model. In your presentation I came across the following dynamic
selection.

underprot = insolidangle center com of lipids span group "Protein" cutoff 5;

I know the purpose of the above statement but I didn't get the meaning of
some of the words, like "insolidangle" and "cutoff=5". If don't mind, can
you please explain this statement?

There are some useful tools for spherical systems like g_jumpdist, g_rdf
(modified)etc that you explained in your presentation. Do you have any
modified gromacs copy with the inclusion of these tools. Because these
tools are very important for my system. Sorry for such a lengthy mail.

Thank you for your time and concern

Venkat
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Re: [gmx-users] Problem with g_chi options

2014-07-09 Thread Justin Lemkul




On 7/9/14, 5:51 AM, Anna Stopka wrote:

Hi everybody,

I wrote last week, but nobody answered. So I write again, still having the same
problem:

I want do an analysis of my simulation with the tool g_chi.
The problem is, that the optional output options don't work.

I use the following command:

g_chi -s config.gro -f traj.xtc -oh -all

and all I get are the standard output files chi.log and order.xvg.
I am not sure if it has something to do with the following warning I get:

WARNING: not all dihedrals found in topology (only 1056 out of 1746)!

Honestly, I don't understand why I get this warning, because all the
input files are fine.



Have you tried using a .tpr file instead of a .gro file as the structure passed 
to -s?  I don't know how there can be any interpretation of a topology, given 
the fact that you haven't passed any topological information to g_chi.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] Fwd: DSSP- error

2014-07-09 Thread Justin Lemkul




On 7/9/14, 8:37 AM, Uma Devi wrote:

Dear gromacs users,
i am using gromacs 4.6.2. i tried the secondary structure analysis, using
do_dssp. but i got the following error.
Fatal error:
Failed to execute command: /usr/local/bin/dssp.exe -na ddFyZGQ1 ddTj0ABl >
/dev/null 2> /dev/null.

i am using amd, with cemtos. i downloaded dssp executable, then placed it
in /usr/local/bin.
i gave permission using chmod a+x dssp.
then i export dssp from my folder using
export DSSP=/usr/local/bin/dssp
please help me to sort it out the problem



Did you do what I suggested to you earlier by making sure you set the DSSP 
environment variable correctly?  do_dssp shouldn't be trying to execute dssp.exe 
if you told it to use dssp.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Re: [gmx-users] Passing group of solvent molecules by argument in genion

2014-07-09 Thread Justin Lemkul




On 7/9/14, 8:46 AM, Marco Rougeth wrote:

Hello people,

is there any way of pass what group of solvent I want to use in *genion*?
I'm creating a non-interactive script that calls genion, any thoughts about
how I would solve it?



genion works like any other command in that regard.

http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

Using group names here is the easiest way to go, e.g.

echo "SOL" | genion ...

-Justin

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Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
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Re: [gmx-users] Graphene topology file

2014-07-09 Thread Justin Lemkul




On 7/9/14, 9:06 AM, #SUKRITI GUPTA# wrote:

Thanks for the reply Justin. I just checked my box size again and found it to
be smaller than the required. Hence I changed the size and ran the simulation
again. This time energy minimization happened correctly without any change in
the graphene structure. But when I am doing npt, the water is suddenly moving
far away from the graphene sheet any tries to agglomerate together causing
the box size to increase drastically. It is almost like the box is about to
explode. Its size changes from 2.5A to 11A.

Can you please help me figure out the problem.



Does the box expand along z?  Are you using walls?  If not, you should be, in 
the case of pbc = xy.


-Justin

--
==

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Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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Re: [gmx-users] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters

2014-07-09 Thread Justin Lemkul




On 7/9/14, 10:11 AM, Nikolaos Michelarakis wrote:

Hey,

Thanks a lot, I fixed the file but I am now getting a python error, I think.

Traceback (most recent call last):
   File "./cgenff_charmm2gmx.py", line 792, in 
 m.read_mol2_coor_only(mol2_name)
   File "./cgenff_charmm2gmx.py", line 720, in read_mol2_coor_only
 atomi = int(entry[0])-1
ValueError: invalid literal for int() with base 10: ''

something wrong with the coordinates?

the new mol2 file is:

https://drive.google.com/file/d/0BzqRbRx4Ynf0SV9rZnhhTmxGRmM/edit?usp=sharing



I'll have to dig into this a bit more closely, but it's not something I have 
time for at the moment.  Adding some print statements to the Python script will 
tell you exactly what's going on.


Also note that your mol2 file will still generate problems because all of your H 
atoms are named simply "H" rather than the actual name assigned in the .str 
file, so you're going to have problems there, as well.  The script is intended 
to parse the matching output from a mol2 file submitted to ParamChem, so any 
other use of the script will require some occasional hacking, workarounds, or 
caveats for input files.


-Justin

--
==

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Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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Re: [gmx-users] Passing group of solvent molecules by argument in genion

2014-07-09 Thread Marco Rougeth

That's the answer! Thank you Justin.

Marco.


2014-07-09 14:25 GMT-03:00 Justin Lemkul :

>
>
> On 7/9/14, 8:46 AM, Marco Rougeth wrote:
>
>> Hello people,
>>
>> is there any way of pass what group of solvent I want to use in *genion*?
>>
>> I'm creating a non-interactive script that calls genion, any thoughts
>> about
>> how I would solve it?
>>
>>
> genion works like any other command in that regard.
>
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
>
> Using group names here is the easiest way to go, e.g.
>
> echo "SOL" | genion ...
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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] 3dc + GPU

2014-07-09 Thread Ondrej Kroutil

Hi gromacs users and developers,
I have troubles with simulations of the system with surface (slab geometry)
using GPU and Verlet cut-off scheme.
When I run this simulation on CPU everything goes right and ions dissolved
in the water above the surface seems to behave normally. But when I switch
to GPU positively charged ions move in z-direction to the bottom of the
simulation box and negatively charged ions go to opposite side of the box.
I have had this problem with 4.6 version and now even with version 5.0.
Do you have any suggestion what can be wrong? Bad input parameters? Etc.
You can download tar file with input file, .tpr file (if you want to run it
on your system, output log and pictures of initial and final state)

https://drive.google.com/file/d/0Byl8CD_rdzQOZVB2UGVHQzllMms/edit?usp=sharing

Thank you very much and keep developing Gromacs, the best simulation
package ever!

Ondřej

Btw.: How can I set-up in gromacs-5.0 to run simulations only on CPU?

-- 
Ondřej Kroutil
,,  Faculty of Health and Social Studies
   "))' University of South Bohemia
 OOO   Jirovcova 24, Ceske Budejovice
  OOO  The Czech Republic
| OO E-mail:  okrou...@gmail.com
>--O Mobile:  +420 736 537 190
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Re: [gmx-users] Tutorial updates

2014-07-09 Thread Oliver Stueker

Hi Justin,

Do you plan to keep the Gromacs 4.x versions of your tutorials (which by
the way are excellent) around for a little longer as well?

>From my experience It will still take quite some time until Gromacs 5 is
available on most Clusters and Linux-package repositories, whereas the
Gromacs 4 versions are readily available.


Best,
Oliver



On Mon, Jul 7, 2014 at 7:48 AM, Justin Lemkul  wrote:

>
> All,
>
> For anyone using my tutorials, you will notice some changes in the coming
> days.  I am updating all of them to be compatible with the newly released
> Gromacs version 5.0.  Most of these changes will be superficial, such as
> small changes to command names or options.  I have already updated all of
> the tutorials except the ones related to free energy calculations, since
> these will require the greatest amount of work given the changes in .mdp
> options.
>
> Be advised that content will be somewhat fluid over the next few days, as
> I find time to make the necessary changes.  Feedback on clarity and
> correctness is always welcome.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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] 3dc + GPU

2014-07-09 Thread Mark Abraham

On Jul 9, 2014 7:39 PM, "Ondrej Kroutil"  wrote:
>
> Hi gromacs users and developers,
> I have troubles with simulations of the system with surface (slab
geometry)
> using GPU and Verlet cut-off scheme.
> When I run this simulation on CPU everything goes right and ions dissolved
> in the water above the surface seems to behave normally. But when I switch
> to GPU positively charged ions move in z-direction to the bottom of the
> simulation box and negatively charged ions go to opposite side of the box.
> I have had this problem with 4.6 version and now even with version 5.0.
> Do you have any suggestion what can be wrong? Bad input parameters? Etc.
> You can download tar file with input file, .tpr file (if you want to run
it
> on your system, output log and pictures of initial and final state)
>
>
https://drive.google.com/file/d/0Byl8CD_rdzQOZVB2UGVHQzllMms/edit?usp=sharing
>
> Thank you very much and keep developing Gromacs, the best simulation
> package ever!
>
> Ondřej
>
> Btw.: How can I set-up in gromacs-5.0 to run simulations only on CPU?

No idea for the main issue, but cmake -DGMX_GPU=off or running as mdrun -nb
CPU are different ways to do what you want.

Mark

> --
> Ondřej Kroutil
> ,,  Faculty of Health and Social Studies
>"))' University of South Bohemia
>  OOO   Jirovcova 24, Ceske Budejovice
>   OOO  The Czech Republic
> | OO E-mail:  okrou...@gmail.com
> >--O Mobile:  +420 736 537 190
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[gmx-users] Question about "atom" field in .top / .itp file vs ffnonbonded.itp

2014-07-09 Thread Eric Smoll

Hello Gromacs Users,

Can the atom field (e.g., "H") of a .top / .itp file differ from the atom
field of the .gro file and, for instance, the ffnonbonded.itp file?  What
are the restrictions here?

My guess is that the .top /.itp will reference with the ffnonbonded.itp
with the type field only (e.g., opls_900). But can the atom tags differ
between these two files ("HA" vs "H", for instance). Can both atom tags
differ from the tags in the .gro file?

-Eric
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Re: [gmx-users] Tutorial updates

2014-07-09 Thread Justin Lemkul




On 7/9/14, 2:40 PM, Oliver Stueker wrote:

Hi Justin,

Do you plan to keep the Gromacs 4.x versions of your tutorials (which by
the way are excellent) around for a little longer as well?

 From my experience It will still take quite some time until Gromacs 5 is
available on most Clusters and Linux-package repositories, whereas the
Gromacs 4 versions are readily available.



The old tutorials are (mostly) still available.  Just append "_old" to the URL 
for the tutorial title, e.g. "lysozyme_old" in place of just "lysozyme."  A 
couple of the tutorials I simply converted (vsites and biphasic) because there 
are so few steps (they are hardly "tutorials," just demonstrations) that there 
was no sense in making a "backup" for the old version.


Ultimately, the old versions will go away.  There's already a large amount of 
upkeep and user feedback to take care of, and I simply don't have time to keep 
track of multiple versions of things.


Additionally, anyone who has worked through any of the tutorials who would like 
to look through the new ones to make sure everything makes sense - feedback 
would be appreciated.  I'm basically just converting command syntax and updating 
.mdp files, but I'm not regenerating all of the data, so if anything is going 
haywire, I don't know yet :)


-Justin



Best,
Oliver



On Mon, Jul 7, 2014 at 7:48 AM, Justin Lemkul  wrote:



All,

For anyone using my tutorials, you will notice some changes in the coming
days.  I am updating all of them to be compatible with the newly released
Gromacs version 5.0.  Most of these changes will be superficial, such as
small changes to command names or options.  I have already updated all of
the tutorials except the ones related to free energy calculations, since
these will require the greatest amount of work given the changes in .mdp
options.

Be advised that content will be somewhat fluid over the next few days, as
I find time to make the necessary changes.  Feedback on clarity and
correctness is always welcome.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Question about "atom" field in .top / .itp file vs ffnonbonded.itp

2014-07-09 Thread Justin Lemkul




On 7/9/14, 5:08 PM, Eric Smoll wrote:

Hello Gromacs Users,

Can the atom field (e.g., "H") of a .top / .itp file differ from the atom
field of the .gro file and, for instance, the ffnonbonded.itp file?  What
are the restrictions here?

My guess is that the .top /.itp will reference with the ffnonbonded.itp
with the type field only (e.g., opls_900). But can the atom tags differ
between these two files ("HA" vs "H", for instance). Can both atom tags
differ from the tags in the .gro file?



The second column of ffnonbonded.itp has nothing to do (directly) with system 
topologies or coordinate files.  It is a bonded atom type (hence the column 
title "bond_type"), which is a translated type used in ffbonded.itp.  Since 
there are far fewer bond types than there are nonbonded types, this keeps the 
files compact by avoiding unnecessary redundancy in ffbonded.itp.


-Justin


--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] mdrun error messages

2014-07-09 Thread Andy Chao

Dear GROMACS Users:

I used the grompp command to run energy minimization of an ionic liquid
structure according to the following command:

grompp -f em.mdp -c C4mimNTf2.gro -p C4mimNTf2.top -o NPT.tpr

and then run molecular dynamics simulation as the following:

mdrun -s NPT.tpr -o NPT.trr

when I opend the NPT.trr file, there is nothing inside.  Can you explain
what was wrong?

The last part of the md.log file shows
Initialized non-bonded Ewald correction tables, spacing: 6.26e-04 size: 3836

Pinning threads with an auto-selected logical core stride of 1

Initializing LinNear Constraints Solver


Thanks!

Andy
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[gmx-users] MDRUN error message

2014-07-09 Thread Andy Chao

Dear GROMACS Users:

I used the grompp command to run energy minimization of an ionic liquid
structure according to the following command:

grompp -f em.mdp -c C4mimNTf2.gro -p C4mimNTf2.top -o NPT.tpr

and then run molecular dynamics simulation as the following:

mdrun -s NPT.tpr -o NPT.trr

when I opend the NPT.trr file, there is nothing inside.  Can you explain
what was wrong?

The last part of the md.log file shows
Initialized non-bonded Ewald correction tables, spacing: 6.26e-04 size: 3836

Pinning threads with an auto-selected logical core stride of 1

Initializing LinNear Constraints Solver


Thanks!
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Re: [gmx-users] Regarding 'insolidangle' and some tools

2014-07-09 Thread Teemu Murtola

Hi,

On Wed, Jul 9, 2014 at 7:13 PM, Venkat Reddy  wrote:

> underprot = insolidangle center com of lipids span group "Protein" cutoff
> 5;
>
> I know the purpose of the above statement but I didn't get the meaning of
> some of the words, like "insolidangle" and "cutoff=5". If don't mind, can
> you please explain this statement?
>

Please see 'gmx help selections keywords insolidangle' for a general
explanation. If that is not clear, I can clarify that further.

There are some useful tools for spherical systems like g_jumpdist, g_rdf
> (modified)etc that you explained in your presentation. Do you have any
> modified gromacs copy with the inclusion of these tools. Because these
> tools are very important for my system. Sorry for such a lengthy mail.
>

I have sent whatever I had for these tools to you personally in May 2013.
Not much has happened since, except that 'gmx distance', 'gmx gangle' and
'gmx sasa' may be able to cover some parts of the needs. Due to various
reasons (most important of which is that I have left academia in 2010), it
has not been exactly fast to get any of those tools actually included in
Gromacs.

I never had "modified Gromacs copy", but only a set of tools and the
selection engine that could be compiled against an existing Gromacs
installation. The selection engine was included in Gromacs 4.5, and the
code has changed a lot since, but the tools have not been updated and so do
not work with newer Gromacs versions without modifications.
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Re: [gmx-users] Problems in compiling GROMACS with VMD plugin (Roland Schulz)

2014-07-09 Thread Roland Schulz

Hi,

are you building with shared-libs (BUILD_SHARED_LIBS=ON)? Is this on Linux?
Is GMX_USE_PLUGINS defined in config.h?

Roland


On Wed, Jul 9, 2014 at 6:15 AM, ming ma  wrote:

> Hi Roland
>
> Now I know how to reply more specifically. Here is the email I sent
> yesterday :)
>
> Thanks for your reply.
>
> >> GMX_USE_PLUGINS has to be enabled in your CMackeCache.txt. Are you
> building
> >> under Linux? It probably didn't find dlopen support. Look for "Result of
> >> test for dlopen" when you run cmake in a new build folder. You can see
> in
> >> CMakeFiles/CMakeError.log why the dlopen test fails.
>
> First, I need to apologize as I don't know how to reply to the contents
> related to my questions only (my thread), so I just replied here directly.
>
> First question, how can I enabled GMX_USE_PLUGINS? Intuitively, I edit the
> file in gromacs-xxx/build/CMakeCache.txt manually by
> setting GMX_USE_PLUGINS fro m OFF to ON.
>
> However, it doesn't work. I first grep PLUGINS in CMakeCache.txt, and got
> the following results
>
> [ming@mingtlv myserial]$ grep PLUGINS CMakeCache.txt
> GMX_LOAD_PLUGINS:BOOL=ON
> //ADVANCED property for variable: GMX_LOAD_PLUGINS
> GMX_LOAD_PLUGINS-ADVANCED:INTERNAL=1
> GMX_USE_PLUGINS:INTERNAL=OFF
>
>
> From the last line, it seems that GROMACS didn't build with PLUGINS, though
> the first one is ON.
>
> Then I grepped dlopen, DLOPEN, vmd, VMD, PLUGINS, plugins in both
> CMakeFiles/CMakeError.log and found nothing.
>
> In the output of cmake, I found the following things for dlopen, DLOPEN and
> vmd.
>
> [ming@mingtlv gromacs-4.6.5]$ grep dlopen s.log
> -- Checking for dlopen
> -- Checking for dlopen - found
> [  3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmddlopen.c.o
>
> [ming@mingtlv gromacs-4.6.5]$ grep DLOPEN s.log
> -- Performing Test HAVE_DLOPEN
> -- Performing Test HAVE_DLOPEN - Success
>
> [ming@mingtlv gromacs-4.6.5]$ grep vmd s.log
> [  3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmddlopen.c.o
> [  6%] Building C object src/gmxlib/CMakeFiles/gmx.dir/vmdio.c.o
>
> So, I still have no idea what's the problem Any suggestions?
>
> Best
> Ming
>
>
> 2014-07-08 21:34 GMT+03:00 <
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se>:
>
> > Send gromacs.org_gmx-users mailing list submissions to
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> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gromacs.org_gmx-users digest..."
> >
> >
> > Today's Topics:
> >
> >1. Re: gmx-5.0 features (Szil?rd P?ll)
> >2. Re: gmx-5.0 features (Szil?rd P?ll)
> >3. Re: hardware setup for gmx (Szil?rd P?ll)
> >4. Re: hardware setup for gmx (Szil?rd P?ll)
> >5. Re: strange but true : How to explain and avoid? (Justin Lemkul)
> >6. Re: Problems in compiling GROMACS with VMD plugin (Roland Schulz)
> >
> >
> > --
> >
> > Message: 1
> > Date: Tue, 8 Jul 2014 19:25:42 +0200
> > From: Szil?rd P?ll 
> > To: gmx-us...@gromacs.org, Michael Brunsteiner 
> > Cc: "gromacs.org_gmx-users@maillist.sys.kth.se"
> > 
> > Subject: Re: [gmx-users] gmx-5.0 features
> > Message-ID:
> >  > egxq8...@mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > On Thu, Jul 3, 2014 at 4:05 PM, Michael Brunsteiner 
> > wrote:
> >
> > >
> > >
> > > Hi,
> > >
> > > I am sorry in case I overlooked the answers in the release-notes,
> > > but I didn't find there answers to:
> > > 1) does gmx-5.0 support free energy calculations + GPU ?
> > >
> >
> > Yes.
> >
> >
> > >
> > > 2) does gmx-5.0 support double precision + GPU ?
> > >
> >
> > No.
> >
> > Cheers,
> > --
> > Szil?rd
> >
> >
> > >
> > > cheers
> > > michael
> > >
> > > ===
> > >
> > >
> > > Why be happy when you could be normal?
> > > --
> > > 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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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > P?ll Szil?rd
> >
> >
> > --
> >
> > Message: 2
> > Date: Tue, 8 Jul 2014 19:25:42 +0200
> > From: Szil?rd P?ll 
> > To: gmx-us...@gromacs.org, Michael Brunsteiner 
> > Cc: "gromacs.org_gmx-users@maillist.sys.kth.se"
> > 
> > Subject: Re: [gmx-users] gmx-5.0 features
> > Message-ID

Re: [gmx-users] Error in system_inflate.gro coordinates does not match

2014-07-09 Thread RINU KHATTRI

hello gromacs users
ohk justin but if unk is deleted then how to put it back in
system_inflate.gro


On Wed, Jul 9, 2014 at 5:16 PM, Justin Lemkul  wrote:

>
>
> On 7/9/14, 6:17 AM, RINU KHATTRI wrote:
>
>> hello every one
>> I am working on complex with popc membrane i did
>>
>> perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat
>>
>> after this step minimization
>>
>> grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
>>
>> i got error
>> Fatal error:
>> number of coordinates in coordinate file (system_inflated.gro, 10224)
>>   does not match topology (topol.top, 10245)
>> i have been removed 6 lipid molecules in my topology file according to
>> output i got one thing new in my system_inflate.gro file the written
>> displayed atom is 10224 but after counting it is 10536 so if i correct it
>> difference is more
>>
>
> I don't know what this means, but the number of atoms that grompp is
> finding is going to be correct.
>
>
>  in topology file [molecule]
>> protein chain 1
>> UNK1
>> POPC 122
>> how to resolve  it
>>
>
> I would venture a guess that UNK has 21 atoms.  I don't know that
> InflateGRO handles arbitrary molecules, so it may have gotten deleted upon
> inflation. Check system_inflated.gro; it will be very obvious if it is
> missing.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> 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] Error in system_inflate.gro coordinates does not match

2014-07-09 Thread RINU KHATTRI

hello every one
ohk i havbben pasted UNK portion from old files because it is still missing
in system.gro now after running minimization i got new error old problem
has resolved
 :-)  grompp  (-:

Option Filename  Type Description

  -f  minim.mdp  Inputgrompp input file with MD parameters
 -po  mdout.mdp  Output   grompp input file with MD parameters
  -c system_inflated.gro  InputStructure file: gro g96 pdb tpr etc.
  -r   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
 -rb   conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr etc.
  -n  index.ndx  Input, Opt.  Index file
  -p  topol.top  InputTopology file
 -pp  processed.top  Output, Opt. Topology file
  -oconfout.tpr  Output   Run input file: tpr tpb tpa
  -t   traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e   ener.edr  Input, Opt.  Energy file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint0   Set the nicelevel
-[no]v   bool   no  Be loud and noisy
-timereal   -1  Take frame at or first after this time.
-[no]rmvsbds bool   yes Remove constant bonded interactions with virtual
sites
-maxwarn int2   Number of allowed warnings during input
processing. Not for normal use and may generate
unstable systems
-[no]zerobool   no  Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum   bool   yes Renumber atomtypes and minimize number of
atomtypes


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#
Generated 813 of the 2346 non-bonded parameter combinations

ERROR 1 [file topol.top, line 22752]:
  No default Proper Dih. types

Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'UNK'
Excluding 3 bonded neighbours molecule type 'POPC'

NOTE 1 [file topol.top, line 24831]:
  System has non-zero total charge: 14.788998
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.


There was 1 note

---
Program grompp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line:
1388

Fatal error:
There was 1 error in input file(s)

kindly help



On Thu, Jul 10, 2014 at 10:17 AM, RINU KHATTRI 
wrote:

> hello gromacs users
> ohk justin but if unk is deleted then how to put it back in
> system_inflate.gro
>
>
> On Wed, Jul 9, 2014 at 5:16 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 7/9/14, 6:17 AM, RINU KHATTRI wrote:
>>
>>> hello every one
>>> I am working on complex with popc membrane i did
>>>
>>> perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat
>>>
>>> after this step minimization
>>>
>>> grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
>>>
>>> i got error
>>> Fatal error:
>>> number of coordinates in coordinate file (system_inflated.gro, 10224)
>>>   does not match topology (topol.top, 10245)
>>> i have been removed 6 lipid molecules in my topology file according to
>>> output i got one thing new in my system_inflate.gro file the written
>>> displayed atom is 10224 but after counting it is 10536 so if i correct it
>>> difference is more
>>>
>>
>> I don't know what this means, but the number of atoms that grompp is
>> finding is going to be correct.
>>
>>
>>  in topology file [molecule]
>>> protein chain 1
>>> UNK1
>>> POPC 122
>>> how to resolve  it
>>>
>>
>> I would venture a guess that UNK has 21 atoms.  I don't know that
>> InflateGRO handles arbitrary molecules, so it may have gotten deleted upon
>> inflation. Check system_inflated.gro; it will be very obvious if it is
>> missing.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>> --
>> 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.

Re: [gmx-users] Graphene topology file

2014-07-09 Thread #SUKRITI GUPTA#

Hi Justin,

I did simulation 2 times, once with PBC in xy with walls and other time with 
pbc in xyz.

For pbc in xy with walls with following wall parameters:

nwall = 2
wall_type = 12-6
wall_density = 5 5
wall_atomtype = opls_995 opls_996
wall_r_linpot = 1
wall_ewald_zfac = 3

Energy minimization runs fine but npt shows following errror and is terminated:

Step 20:
The charge group starting at atom 796 moved than the distance allowed by the 
domain decomposition in direction X
distance out of cell -0.290927
New coordinates:2.4112.0060.982
Old cell boundaries in direction X:0.0002.702
New cell boundaries in direction X:0.0002.702
---
Program mdrun, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 4124

Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

For pbc in xyz, both energy minimization and npt run but the water is suddenly 
moving far away from the graphene sheet any tries to agglomerate together 
causing the box size to increase drastically. It is almost like the box is 
about to explode. Its size changes from  (2.70200   2.55300   4.0) to  
(11.46117  10.82915  16.96695). The box expands in x,y and z all directions.

Thanks and Regards
Sukriti

Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | 
Nanyang Technological University
Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, 
Singapore(637459)
Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg

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

Sent: Thursday, July 10, 2014 1:26 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Graphene topology file

On 7/9/14, 9:06 AM, #SUKRITI GUPTA# wrote:
> Thanks for the reply Justin. I just checked my box size again and found it to
> be smaller than the required. Hence I changed the size and ran the simulation
> again. This time energy minimization happened correctly without any change in
> the graphene structure. But when I am doing npt, the water is suddenly moving
> far away from the graphene sheet any tries to agglomerate together causing
> the box size to increase drastically. It is almost like the box is about to
> explode. Its size changes from 2.5A to 11A.
>
> Can you please help me figure out the problem.
>

Does the box expand along z?  Are you using walls?  If not, you should be, in
the case of pbc = xy.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] How to calculate the COM and box vectors in umbrella sampling

2014-07-09 Thread Maziya Ibrahim

Dear all,

I want to carry out umbrella sampling on a protein-ligand complex, that was
already subjected to regular MD simulation for a few nanoseconds.

How should I calculate the optimum pull distance and box size to be used?
Is there a default value that can be applied?
Also how to calculate the center of mass of the protein and the box vectors?

Any suggestions?
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Re: [gmx-users] Regarding 'insolidangle' and some tools

2014-07-09 Thread Venkat Reddy

Thank you Sir. gmx help explains it. I tried to compile the tools on
gromacs-4.5 but somehow the installation was terminating with errors. Then
I thought, you might have the modified gromacs copy. Anyway, I will try to
install the tools on gromacs-4.5 template. Thank you sir for your time and
concern.


On Thu, Jul 10, 2014 at 9:51 AM, Teemu Murtola 
wrote:

> Hi,
>
>
> On Wed, Jul 9, 2014 at 7:13 PM, Venkat Reddy  wrote:
>
> > underprot = insolidangle center com of lipids span group "Protein" cutoff
> > 5;
> >
> > I know the purpose of the above statement but I didn't get the meaning of
> > some of the words, like "insolidangle" and "cutoff=5". If don't mind, can
> > you please explain this statement?
> >
>
> Please see 'gmx help selections keywords insolidangle' for a general
> explanation. If that is not clear, I can clarify that further.
>
> There are some useful tools for spherical systems like g_jumpdist, g_rdf
> > (modified)etc that you explained in your presentation. Do you have
> any
> > modified gromacs copy with the inclusion of these tools. Because these
> > tools are very important for my system. Sorry for such a lengthy mail.
> >
>
> I have sent whatever I had for these tools to you personally in May 2013.
> Not much has happened since, except that 'gmx distance', 'gmx gangle' and
> 'gmx sasa' may be able to cover some parts of the needs. Due to various
> reasons (most important of which is that I have left academia in 2010), it
> has not been exactly fast to get any of those tools actually included in
> Gromacs.
>
> I never had "modified Gromacs copy", but only a set of tools and the
> selection engine that could be compiled against an existing Gromacs
> installation. The selection engine was included in Gromacs 4.5, and the
> code has changed a lot since, but the tools have not been updated and so do
> not work with newer Gromacs versions without modifications.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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