date:20130408

 Hi, is it possible to instruct gromacs to only perform the dynamics on
 half of the system or protein while ignoring the rest?

 thanks



Would you explain to us why you need so exotic setup?

Dr. Vitaly Chaban
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[gmx-users] Re: can we use GPU from another machine for calculation?

 I've got two GPU workstation both of which have two GTX690 GPU. Now
 I am planning to run Gromacs GPU version and I am just wondering can we
 submit a single GPU jobs in one machine and evoke all GPU resources from
 both machine?


If I were you, I would insert both cards into the same block...

I am not an expert in this question, but intuitively the bandwidth between
your two workstations will likely kill most of the anticipated performance
gain.

Dr. Vitaly Chaban
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[gmx-users] Lipids and virtual site in 4.6.1

2013-04-08 Thread Bastien Loubet

Dear GROMACS user,

Last week I was watching the GTC talk from Eric Lindahl, and I noticed his
insistence on virtual site to accelerate simulation (up to 5ps time step).

As a matter of fact our group recently tried to use virtual site on CHARMM36
POPC bilayer and the result where less than stellar.

We first did a simulation of a POPC bilayer comparing area per lipid with
and without virtual site using GROMACS 4.5.5.
We obtained an area per lipid around 0.62 nm^2 per lipid with no virtual
site but with virtual site we obtained an area per lipid of more than 0.7
nm^2.
After that we found that there was a bug report for the virial calculation
with virtual site in version 4.5: http://redmine.gromacs.org/issues/908

The issue being marked as resolved for 4.6 and we tried our hand at both the
beta3 and 4.6.1 version of it. The result where better but not perfect: we
get 0.65~0.66 nm^2 per lipid.

The problem here is that in order to increase the time step we need all
hydrogen to be virtual sites, so this include the lipids hydrogen and not
just the protein. However if the area per lipid is wrong the stress profile
is likely to be changed, which will affect transmembrane proteins. So we do
not feel confident about using virtual sites in our lipid simulation.

I signal it here because there is a possibility that this is still a bug, If
somebody could confirm/infirm that it would be nice.

Best,

Bastien



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[gmx-users] Re: Simulating a large system

2013-04-08 Thread Juan Antonio Raygoza Garay

Sure, it's basically improving minimization time. if i can focus all my 
resources in simulating or minimizing a portion of the system while ignoring 
other parts that are too far away from the selected portion, it can also be 
possible to run some simulations without the need of a big cluster and sort of 
obtaining about the same results. This goes to my interest of harnessing small 
computing systems for doing all these tasks. There are systems like rna 
molecules where i could get the fine grained structure first and then running 
the entire molecule to obtain the coarser structure.

As someone says it might not improve time but at least having the ability to 
run portions only on my small desktop overnight or just leave it there running 
a lot of this could be accomplished. I do have access to a cluster but having 
to wait in the queue is time that can be used to getting somewhere, maybe 
slower but you're moving.


On Apr 8, 2013, at 5:20 AM, Dr. Vitaly Chaban wrote:

 Vitaly Chaban

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Re: [gmx-users] Lipids and virtual site in 4.6.1

2013-04-08 Thread David van der Spoel


On 2013-04-08 11:34, Bastien Loubet wrote:

Dear GROMACS user,

Last week I was watching the GTC talk from Eric Lindahl, and I noticed his
insistence on virtual site to accelerate simulation (up to 5ps time step).

As a matter of fact our group recently tried to use virtual site on CHARMM36
POPC bilayer and the result where less than stellar.

We first did a simulation of a POPC bilayer comparing area per lipid with
and without virtual site using GROMACS 4.5.5.
We obtained an area per lipid around 0.62 nm^2 per lipid with no virtual
site but with virtual site we obtained an area per lipid of more than 0.7
nm^2.
After that we found that there was a bug report for the virial calculation
with virtual site in version 4.5: http://redmine.gromacs.org/issues/908

The issue being marked as resolved for 4.6 and we tried our hand at both the
beta3 and 4.6.1 version of it. The result where better but not perfect: we
get 0.65~0.66 nm^2 per lipid.

The problem here is that in order to increase the time step we need all
hydrogen to be virtual sites, so this include the lipids hydrogen and not
just the protein. However if the area per lipid is wrong the stress profile
is likely to be changed, which will affect transmembrane proteins. So we do
not feel confident about using virtual sites in our lipid simulation.

I signal it here because there is a possibility that this is still a bug, If
somebody could confirm/infirm that it would be nice.


Did you also try to use vsites without increasing the time step, in 
order to rule out that this is a time step effect rather than a vsite 
effect?




Best,

Bastien



--
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: Fw: [gmx-users] water molecule can not be settled

2013-04-08 Thread Anirban

I thought the sole purpose of open source discussions and sharing is to
help any scientific (or other) community to grow and benefit from each
other, without taking into account the Nationality of the beneficiaries. If
someone is willingly helping out somebody, whether Indian or not, in the
GROMACS forum, then it should not bother Mr. Luis Felipe Pineda de Castro,
since to the best of my knowledge it is not affecting him. I would request
the moderators of this forum to take adequate measures about such postings
as Mr. Castro's.

Regards,

Anirban

On Fri, Apr 5, 2013 at 10:55 PM, Luis Felipe Pineda de Castro 
luis.pinedadecas...@lnu.se wrote:

 After having followed for longer time the queries sent by some Indian
 fellows, I wonder if it wouldn't more effective to arrange for a GROMACS
 tutorial offered by Justin in an Indian location. Maybe you, the Indian
 fellows, can arrange for the financing and invite Justin to hold such a
 Tutorial on the  basics of MD simulations and their implementation in
 GROMACS. Considering the time Justin is spending responding to your
 queries, maybe because you are devoid of adequate supervision or
 theoretical background, this would be only fair. This posting is maybe a
 little bit off topic, but somehow related.

 
 From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
 behalf of Shima Arasteh [shima_arasteh2...@yahoo.com]
 Sent: Friday, April 05, 2013 5:22 PM
 To: Discussion list for GROMACS users
 Subject: Re: Fw: [gmx-users] water molecule can not be settled

 You mean start over the NPT step?



 Sincerely,
 Shima


 - Original Message -
 From: Justin Lemkul jalem...@vt.edu
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Cc:
 Sent: Friday, April 5, 2013 7:50 PM
 Subject: Re: Fw: [gmx-users] water molecule can not be settled

 On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh
 shima_arasteh2...@yahoo.comwrote:

  As I visualized the system, I see a water molecule somewhere between
 lipid
  chains near the protein entrance. This has been happen during NPT. I' d
  like to delete this molecule but with such a kind of fatal error this
 would
  impossible. So what's the way?  Is there any tricky way to change
  coordinate of molecule? but I seems also impossible becasue PME problem!
  So whats the solution?
 
 
 Delete the molecule, adjust your topology (and index file, if necessary),
 and start over with the equilibration.

 -Justin

 --

 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540)
 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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[gmx-users] Re: Simulating a large system

If you do not care about the atoms, which are too far away from the region
of interest, is it not reasonable just to cut that useless part? Also,
you may want to look towards implicit solvent simulations.

Dr. Vitaly Chaban


On Mon, Apr 8, 2013 at 11:35 AM, Juan Antonio Raygoza Garay 
raygo...@psu.edu wrote:

 Sure, it's basically improving minimization time. if i can focus all my
 resources in simulating or minimizing a portion of the system while
 ignoring other parts that are too far away from the selected portion, it
 can also be possible to run some simulations without the need of a big
 cluster and sort of obtaining about the same results. This goes to my
 interest of harnessing small computing systems for doing all these tasks.
 There are systems like rna molecules where i could get the fine grained
 structure first and then running the entire molecule to obtain the coarser
 structure.

 As someone says it might not improve time but at least having the ability
 to run portions only on my small desktop overnight or just leave it there
 running a lot of this could be accomplished. I do have access to a cluster
 but having to wait in the queue is time that can be used to getting
 somewhere, maybe slower but you're moving.


 On Apr 8, 2013, at 5:20 AM, Dr. Vitaly Chaban wrote:

 Vitaly Chaban



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Re: [gmx-users] Lipids and virtual site in 4.6.1

2013-04-08 Thread David van der Spoel


On 2013-04-08 11:52, David van der Spoel wrote:

On 2013-04-08 11:34, Bastien Loubet wrote:

Dear GROMACS user,

Last week I was watching the GTC talk from Eric Lindahl, and I noticed
his
insistence on virtual site to accelerate simulation (up to 5ps time
step).

As a matter of fact our group recently tried to use virtual site on
CHARMM36
POPC bilayer and the result where less than stellar.

We first did a simulation of a POPC bilayer comparing area per lipid with
and without virtual site using GROMACS 4.5.5.
We obtained an area per lipid around 0.62 nm^2 per lipid with no virtual
site but with virtual site we obtained an area per lipid of more than 0.7
nm^2.
After that we found that there was a bug report for the virial
calculation
with virtual site in version 4.5: http://redmine.gromacs.org/issues/908

The issue being marked as resolved for 4.6 and we tried our hand at
both the
beta3 and 4.6.1 version of it. The result where better but not
perfect: we
get 0.65~0.66 nm^2 per lipid.

The problem here is that in order to increase the time step we need all
hydrogen to be virtual sites, so this include the lipids hydrogen and not
just the protein. However if the area per lipid is wrong the stress
profile
is likely to be changed, which will affect transmembrane proteins. So
we do
not feel confident about using virtual sites in our lipid simulation.

I signal it here because there is a possibility that this is still a
bug, If
somebody could confirm/infirm that it would be nice.


Did you also try to use vsites without increasing the time step, in
order to rule out that this is a time step effect rather than a vsite
effect?


And by the way, you are welcome to reopen the redmine issue and upload 
file demonstrating the problem.




Best,

Bastien



--
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http://gromacs.5086.n6.nabble.com/Lipids-and-virtual-site-in-4-6-1-tp5007063.html

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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] RDF output has no data

2013-04-08 Thread Venkat Reddy

Sir

I was using an old version. Now I used 4.5.5, it still gives me the same
blank output file.

Kindly suggest how to go about solving this

Thanks


On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham mark.j.abra...@gmail.comwrote:

 On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy venkat...@gmail.com wrote:

  There was no fatal error preceding the output. After selecting the groups
  following are the output on the screen
  Reading frame   1 time0.100
  Warning: can not make broken molecules whole without a run input file,
   don't worry, mdrun doesn't write broken molecules
 

 This message is from a prehistoric version of g_rdf. Please get a new one.

 Mark


 
  Reading frame2000 time  200.000
 
 
  gcq#69: The Wheels On the Bus Go Round and Round (J. Richman)
 
  And the rdf.xvg file looks like this
 
  #This file was created Sat Apr  6 10:54:13 2013
  # by the following command:
  # g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg
  #
  # g_rdf is part of G R O M A C S:
  #
  # GROningen MAchine for Chemical Simulation
  #
  @title Radial Distribution
  @xaxis  label r
  @yaxis  label 
  @TYPE xy
  @ subtitle O21-H2__CAT
   0.001  1
  ~
 
  Whats going wrong? Please help.
 
 
  On Sat, Apr 6, 2013 at 12:41 AM, Justin Lemkul jalem...@vt.edu wrote:
 
   On Fri, Apr 5, 2013 at 2:30 PM, Venkat Reddy venkat...@gmail.com
  wrote:
  
Dear users
   
I have used AMBER MD package to run simulation for a solvent box. I
 am
   now
using the gromacs utility to calculate rdf as follows:
   
g_rdf -f file.trr -s file.pdb -n rdf.ndx -o rdf.xvg
   
However, I get no data in the output rdf.xvg. Since Im using
 specially
generated force field parameters, I do not know how to go about
   generating
a tpr file (in case that is the problem). The rdf.ndx file is correct
  for
my atom selection. Please suggest how to go about solving this.
   
   
   Blank output usually indicates the command failed, which should have
 been
   preceded by a rather obvious fatal error. If a .tpr file is required,
  g_rdf
   will tell you (again, a fatal error).
  
   -Justin
  
   --
  
   
  
   Justin A. Lemkul, Ph.D.
   Research Scientist
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu | (540)
   231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
  
   
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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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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] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L

Dear Qinghua Liao -

In that case, I am just wishing you luck with the copper containing systems.

Are you going to simulate copper-ligand interactions using Coulomb+LJ
potential only? I would guess it is a chemical bonding case. Maybe the
Morse potential (additionally) can be of better service?


Dr. Vitaly Chaban




On Mon, Apr 8, 2013 at 1:09 PM, fantasticqhl fantastic...@gmail.com wrote:

  Dear Dr. Vitaly Chaban,

 Thanks very much for your explanation. I guess that I get what you mean
 now! Thanks!

 All the best,
 Qinghua Liao

 On 04/07/2013 11:35 AM, Dr. Vitaly Chaban wrote:

 The equation is a direct consequence of LJ-12-6 equation. This equation is
 used in OPLS and most other force fields.

  The difference you found originate from the fact that, besides LJ
 potential, there is much stronger Coulomb potential in the copper-ion case.
 If you run simulations, you will see that copper-ligand distance is smaller
 than the sum of their sigmas multiplied by pow (2, 1/6).


  Dr. Vitaly Chaban






  On Sun, Apr 7, 2013 at 11:28 AM, fantasticqhl fantastic...@gmail.comwrote:

  Dear Dr. Vitaly Chaban,

 Thanks for the explanation. I know this equation. However, the van der
 Waals radius and its counterpart sigma in OPLS-AA/L force field files do
 not follow this equation.

 For example, the vdw radius of copper ion is 1.4 angstrom, and its sigma
 is  2.08470e-01 (I guess the unit is nm). pow(2, 1/6) is more than 1, so
 obviously this equation
 does not work with copper. So do other atoms. I guess that there might be
 an additional coefficient for this equation in gromacs. That's the purpose
 for asking. Thanks very much!


 All the best,
 Qinghua

 On 04/07/2013 10:48 AM, Dr. Vitaly Chaban wrote:

 Dear Qinghua -

  The formal relation is diameter = pow (2, 1/6) * sigma, provided that
 you have only LJ potential in your interacting subsystem.

  If this is not the case, an optimal sigma can only be found iteratively.


  Dr. Vitaly Chaban





 On Sun, Apr 7, 2013 at 10:36 AM, fantasticqhl fantastic...@gmail.comwrote:

 Dear Dr. Vitaly Chaban,

 Thanks very much for your reply. My question is the relationship between
 van der Waals radius and sigma in the OPLS-AA/L force filed files of
 Gromacs.

 Of course I did ab initio optimizations of my system, but I do not know
 there is some relation between the optimal bond length (copper--atom of the
 ligand) and sigma.
 Could you please be more clear and give a little detailed explanation?
 Thanks very much!

 All the best,
 Qinghua

 On 04/06/2013 06:07 PM, Dr. Vitaly Chaban wrote:

 In systems of such kind, everything will depend on the atom of the
 ligand,
 which coordinated by copper ion.

 Perform ab initio geometry optimization and find the optimal distance.
 Then
 adjust sigma(s).

 Dr. Vitaly Chaban







 There is a copper ion with four ligands in my system. I am going to

 study this system using MD simulations.
 For the vdW parameters, R*=1.74 angstrom and epsilon=1.14 kcal.mol from
 one paper will be used in our
 simulations. I already found the parameters of copper ion (Cu2+) in the
 OPLS-AA/L force field files:
 sigma= 2.08470e-01, epsilon=4.76976e+00, which are for Cu2+ without
 ligands. The two epsilon are the same,
 just with different units.

 My question is that I do not know how to convert the vdW radius to
 sigma. I found that the vdw radius of copper is
 1.4 angstrom, and the sigma in the force field file is 2.08470e-01.
 Could someone tell me how to do the converting?

 Thanks very much!








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[gmx-users] MD with Xenon

2013-04-08 Thread Divya Sunil

hello,

 I have a protein in which I fixed Xenon in the binding sites. without
xenon, I used GROMOS96 53a6 force field for simulation. With Xenon, which
forcefield am I able to use?

thanking you
regards

Divya
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Re: [gmx-users] GROMACS 4.6v - Myrinet2000

On Mon, Apr 8, 2013 at 2:28 AM, Hrachya Astsatryan hr...@sci.am wrote:

 Dear all,

 We have installed the latest version of Gromacs (version 4.6) on our
 cluster by the following step:

  * cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/**backup/sicnas/gromacs
-DGMX_BUILD_OWN_FFTW=ON -DGMX_PREFER_STATIC_LIBS=ON


With this command, you're building Gromacs' internal FFT rather than using
FFTW. Your performance will be much better if you use FFTW. See the
installation instructions for more information.

-Justin


 The interconnection of the cluster is Myrinet2000 and the driver is MX
 (and mpich 1.3.1).

 The job scripts (see below) and different simulations show that there is
 no adequate performance (usually it should be 2-3 time more).

 Could you, pls. help us to overcome the problem in order to get better
 performance?

 With regards,
 Hrach

 #PBS -l nodes=8:ppn=2
 ##PBS -l walltime=360:00
 #PBS -q armcluster
 #PBS -e 33mM_16_new.err
 #PBS -o 33mM_16_new.log
 ## Specify the shell to be bash
 #PBS -S /bin/bash

 export LD_LIBRARY_PATH=$LD_LIBRARY_**PATH:/backup/sicnas/gromacs/**
 lib:/opt/mpi/lib

 /opt/mpi/bin/mpirun -machinefile /backup/sicnas/npt101/machine -np 16
 /backup/sicnas/gromacs/bin/**mdrun_mpi -s /backup/sicnas/npt101/topol.**tpr
 -v





 --
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Virginia Tech
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Re: [gmx-users] MD with Xenon

2013-04-08 Thread Anirban

On Mon, Apr 8, 2013 at 5:04 PM, Divya Sunil divyasunilku...@gmail.comwrote:

 hello,

  I have a protein in which I fixed Xenon in the binding sites. without
 xenon, I used GROMOS96 53a6 force field for simulation. With Xenon, which
 forcefield am I able to use?


Xenon is a non-standard molecule and you need to derive the parameters for
it (refer to literature). Then you can use those parameters even with the
53a6 FF like any other non-standard molecule.


 thanking you
 regards

 Divya
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Re: [gmx-users] Re: Simulating a large system

On Mon, Apr 8, 2013 at 5:54 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:

 If you do not care about the atoms, which are too far away from the region
 of interest, is it not reasonable just to cut that useless part? Also,


Hear hear. If it's so meaningless, why is it there? ;)


 you may want to look towards implicit solvent simulations.


Indeed. Or use GPU's. Erik was showing us great performance on a laptop
during the webinar, even using (relatively) cheap consumer-grade cards.
Back to the original point (and as I posted before), even if you freeze
some amount of atoms, you don't gain any performance by doing so.

-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] amber99 with berger's lipids

2013-04-08 Thread James Starlight

In literature I found that the ussage of 1.0 cutoffs should give good
results but in the antechamber manual I've seen that usages of 1.2 cutoofs
( with GAFF) should be used. So what cut-offs should I use for
protein-ligand complexes done in amber ? (assuming that I simulate my
system in the berger lipids )



James

2013/4/6 Justin Lemkul jalem...@vt.edu

 On Sat, Apr 6, 2013 at 10:46 AM, Albert mailmd2...@gmail.com wrote:

  On 04/06/2013 04:29 PM, Justin Lemkul wrote:
 
  And what was your basis for that decision?  What makes you think that
  AMBER99 can even be combined with the Berger lipid force field?
 
  -Justin
 
 
 
  I think he probably read this paper which suggest the combination of
 Amber
  FF and Berger lipids FF:
 
  http://pubs.acs.org/doi/abs/**10.1021/ct200491c
 http://pubs.acs.org/doi/abs/10.1021/ct200491c
 

 Fair enough. I wasn't aware of that one. But if that's the case, then I
 suggest James have another read through it, since the cutoffs are described
 explicitly, thus answering his original question.

 -Justin

 --

 

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[gmx-users] Re: RDF output has no data

I believe the problem is in the way which you used to convert AMBER
trajectory to the GROMACS trajectory

I would suggest to try gmxdump and see what your trajectory looks like. Oe
maybe even better - try to visualize it in VMD to see if the format is
correct.

Dr. Vitaly Chaban



Sir

 I was using an old version. Now I used 4.5.5, it still gives me the same
 blank output file.

 Kindly suggest how to go about solving this

 Thanks


 On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

  On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy venkat...@gmail.com
 wrote:
 
   There was no fatal error preceding the output. After selecting the
 groups
   following are the output on the screen
   Reading frame   1 time0.100
   Warning: can not make broken molecules whole without a run input file,
don't worry, mdrun doesn't write broken molecules
  
 
  This message is from a prehistoric version of g_rdf. Please get a new
 one.
 
  Mark
 
 
  
   Reading frame2000 time  200.000
  
  
   gcq#69: The Wheels On the Bus Go Round and Round (J. Richman)
  
   And the rdf.xvg file looks like this
  
   #This file was created Sat Apr  6 10:54:13 2013
   # by the following command:
   # g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg
   #
   # g_rdf is part of G R O M A C S:
   #
   # GROningen MAchine for Chemical Simulation
   #
   @title Radial Distribution
   @xaxis  label r
   @yaxis  label 
   @TYPE xy
   @ subtitle O21-H2__CAT
0.001  1
   ~
  
   Whats going wrong? Please help.

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[gmx-users] Re: Lipids and virtual site in 4.6.1

2013-04-08 Thread Bastien Loubet

Actually we did not increase the time step between the simulations. The plan
was to increase it after we checked the basic properties of the membrane,
but we never got to that point.

I will try to put something together for redmine soon.

Thanks for the answer,

Bastien



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Re: [gmx-users] Simulating a large system

You might use freeze groups or position restraints depending what you want.
See manual.

Mark
On Apr 8, 2013 2:58 AM, Juan Antonio Raygoza Garay raygo...@psu.edu
wrote:

 Hi, is it possible to instruct gromacs to only perform the dynamics on
 half of the system or protein while ignoring the rest?

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Re: [gmx-users] Re: Simulating a large system

Yes, there's no way to cheat on the explicit electrostatics to reduce cost,
except implicit solvation. The kind of approach used in QM/MM is not useful
for MM/MM! The rate-limiting part is still there.

Mark
On Apr 8, 2013 12:42 PM, Justin Lemkul jalem...@vt.edu wrote:

 On Mon, Apr 8, 2013 at 5:54 AM, Dr. Vitaly Chaban vvcha...@gmail.com
 wrote:

  If you do not care about the atoms, which are too far away from the
 region
  of interest, is it not reasonable just to cut that useless part? Also,
 

 Hear hear. If it's so meaningless, why is it there? ;)


  you may want to look towards implicit solvent simulations.
 
 
 Indeed. Or use GPU's. Erik was showing us great performance on a laptop
 during the webinar, even using (relatively) cheap consumer-grade cards.
 Back to the original point (and as I posted before), even if you freeze
 some amount of atoms, you don't gain any performance by doing so.

 -Justin

 --

 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540)
 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
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[gmx-users] Calculation of Temperature of Cluster

Dear All,

I tried to use g_clustsize_d program for estimation of temperature of
cluster/nanodroplet but the temperature output file is empty. Could you
comment where is the problem?

Please note that I can get Temperature of system using g_energy_d but I'm
interest to know cooling effect of nano-drop after evaporation.


Best
Rasoul
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Re: [gmx-users] Calculation of Temperature of Cluster

On Mon, Apr 8, 2013 at 9:01 AM, Rasoul Nasiri nasiri1...@gmail.com wrote:

 Dear All,

 I tried to use g_clustsize_d program for estimation of temperature of
 cluster/nanodroplet but the temperature output file is empty. Could you
 comment where is the problem?


Not without seeing your command line. I'd be willing to guess that you
either used an .xtc file (which does not store velocities) or a .trr that
didn't save velocities (i.e. nstvout = 0).

-Justin


 Please note that I can get Temperature of system using g_energy_d but I'm
 interest to know cooling effect of nano-drop after evaporation.


 Best
 Rasoul
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Department of Biochemistry
Virginia Tech
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231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Calculation of Temperature of Cluster

Bellow is my command which I used:

g_clustsize_d -f traj.xtc  -s topol.tpr -n n.ndx -nc nclust.xvg -mc maxclust
.xvg -ac avclust.xvg -mcn maxclust.ndx -cut 0.516 -temp Tempe.xvg

Rasoul


On Mon, Apr 8, 2013 at 2:04 PM, Justin Lemkul jalem...@vt.edu wrote:

 On Mon, Apr 8, 2013 at 9:01 AM, Rasoul Nasiri nasiri1...@gmail.com
 wrote:

  Dear All,
 
  I tried to use g_clustsize_d program for estimation of temperature of
  cluster/nanodroplet but the temperature output file is empty. Could you
  comment where is the problem?
 
 
 Not without seeing your command line. I'd be willing to guess that you
 either used an .xtc file (which does not store velocities) or a .trr that
 didn't save velocities (i.e. nstvout = 0).

 -Justin


  Please note that I can get Temperature of system using g_energy_d but I'm
  interest to know cooling effect of nano-drop after evaporation.
 
 
  Best
  Rasoul
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 --

 

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 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540)
 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
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Re: [gmx-users] Calculation of Temperature of Cluster

On Mon, Apr 8, 2013 at 9:08 AM, Rasoul Nasiri nasiri1...@gmail.com wrote:

 Bellow is my command which I used:

 g_clustsize_d -f traj.xtc  -s topol.tpr -n n.ndx -nc nclust.xvg -mc
 maxclust
 .xvg -ac avclust.xvg -mcn maxclust.ndx -cut 0.516 -temp Tempe.xvg


Then it is exactly what I said. Temperatures require velocities. Velocities
are not stored in .xtc files and thus you can't extract any temperature
information in this way.

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] amber99 with berger's lipids

On Mon, Apr 8, 2013 at 7:50 AM, James Starlight jmsstarli...@gmail.comwrote:

 In literature I found that the ussage of 1.0 cutoffs should give good
 results but in the antechamber manual I've seen that usages of 1.2 cutoofs
 ( with GAFF) should be used. So what cut-offs should I use for
 protein-ligand complexes done in amber ? (assuming that I simulate my
 system in the berger lipids )



Do a few test runs and see. I would think the cutoff value would more
strongly affect the lipids, not the ligand, whose interactions are
comparatively few and relatively local. If you use the Verlet cutoff scheme
in version 4.6, it's largely irrelevant since there will not be any
missed interactions either way.

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L

2013-04-08 Thread fantasticqhl


Dear Dr. Vitaly Chaban,

Thanks very much for concern on my research! We are going to the use the 
bonded model together with Coulomb and LJ potentials.


My problem is that vdw radius and its sigma do not follow the equation 
of  Rvdw = pow(2, 1/6)*sigma in the OPLS force field files,
not just for copper. That's why I sent these e-mails for suggestions. I 
am sorry for the unclear.


All the best,
Qinghua Liao


On 04/08/2013 01:22 PM, Dr. Vitaly Chaban wrote:

Dear Qinghua Liao -

In that case, I am just wishing you luck with the copper containing 
systems.


Are you going to simulate copper-ligand interactions using Coulomb+LJ 
potential only? I would guess it is a chemical bonding case. Maybe the 
Morse potential (additionally) can be of better service?



Dr. Vitaly Chaban




On Mon, Apr 8, 2013 at 1:09 PM, fantasticqhl fantastic...@gmail.com 
mailto:fantastic...@gmail.com wrote:


Dear Dr. Vitaly Chaban,

Thanks very much for your explanation. I guess that I get what you
mean now! Thanks!

All the best,
Qinghua Liao

On 04/07/2013 11:35 AM, Dr. Vitaly Chaban wrote:

The equation is a direct consequence of LJ-12-6 equation. This
equation is used in OPLS and most other force fields.

The difference you found originate from the fact that, besides LJ
potential, there is much stronger Coulomb potential in the
copper-ion case. If you run simulations, you will see that
copper-ligand distance is smaller than the sum of their sigmas
multiplied by pow (2, 1/6).


Dr. Vitaly Chaban






On Sun, Apr 7, 2013 at 11:28 AM, fantasticqhl
fantastic...@gmail.com mailto:fantastic...@gmail.com wrote:

Dear Dr. Vitaly Chaban,

Thanks for the explanation. I know this equation. However,
the van der Waals radius and its counterpart sigma in
OPLS-AA/L force field files do not follow this equation.

For example, the vdw radius of copper ion is 1.4 angstrom,
and its sigma is 2.08470e-01 (I guess the unit is nm). pow(2,
1/6) is more than 1, so obviously this equation
does not work with copper. So do other atoms. I guess that
there might be an additional coefficient for this equation in
gromacs. That's the purpose for asking. Thanks very much!


All the best,
Qinghua

On 04/07/2013 10:48 AM, Dr. Vitaly Chaban wrote:

Dear Qinghua -

The formal relation is diameter = pow (2, 1/6) * sigma,
provided that you have only LJ potential in your interacting
subsystem.

If this is not the case, an optimal sigma can only be found
iteratively.


Dr. Vitaly Chaban





On Sun, Apr 7, 2013 at 10:36 AM, fantasticqhl
fantastic...@gmail.com mailto:fantastic...@gmail.com wrote:

Dear Dr. Vitaly Chaban,

Thanks very much for your reply. My question is the
relationship between van der Waals radius and sigma in
the OPLS-AA/L force filed files of Gromacs.

Of course I did ab initio optimizations of my system,
but I do not know there is some relation between the
optimal bond length (copper--atom of the ligand) and sigma.
Could you please be more clear and give a little
detailed explanation? Thanks very much!

All the best,
Qinghua

On 04/06/2013 06:07 PM, Dr. Vitaly Chaban wrote:

In systems of such kind, everything will depend on
the atom of the ligand,
which coordinated by copper ion.

Perform ab initio geometry optimization and find the
optimal distance. Then
adjust sigma(s).

Dr. Vitaly Chaban







There is a copper ion with four ligands in my
system. I am going to

study this system using MD simulations.
For the vdW parameters, R*=1.74 angstrom and
epsilon=1.14 kcal.mol from
one paper will be used in our
simulations. I already found the parameters of
copper ion (Cu2+) in the
OPLS-AA/L force field files:
sigma= 2.08470e-01, epsilon=4.76976e+00, which
are for Cu2+ without
ligands. The two epsilon are the same,
just with different units.

My question is that I do not know how to convert
the vdW radius to
sigma. I found that the vdw radius of copper is
1.4 angstrom, and the sigma in the force field
file is 2.08470e-01.
Could someone tell me how to do the converting?

Thanks very much!












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Re: [gmx-users] Restarting a REMD simulation (error)

On Apr 8, 2013 8:53 AM, João Henriques joao.henriques.32...@gmail.com
wrote:

 Dear all,

 Due to cluster wall-time limitations, I was forced to restart two REMD
 simulations. It ran absolutely fine until hitting the wall-time. To
restart
 I used the following command:

 mpirun -np 64 -output-filename MPIoutput $GromDir/mdrun_mpi -s H5_.tpr
 -multi 64 -replex 1000 -deffnm H5_ -cpi -noappend

 (I'm using GMX-4.0.7 and yes I know it's old but I have my own reasons for
 using it.)

 Here is a random replica (#1) MPI output:

 ##START###
 NNODES=64, MYRANK=1, HOSTNAME=an091
 NODEID=1 argc=11
 Checkpoint file is from part 1, new output files will be suffixed
part0002.
 Reading file H5_1.tpr, VERSION 4.0.7 (single precision)

 Reading checkpoint file H5_1.cpt generated: Wed Apr  3 17:13:14 2013

 ---
 Program mdrun_mpi, VERSION 4.0.7
 Source code file: main.c, line: 116

 Fatal error:
 The 64 subsystems are not compatible

 ---

 Error on node 1, will try to stop all the nodes
 Halting parallel program mdrun_mpi on CPU 1 out of 64
 ##END###

 It's reading from the correct cpt and tpr files, so it must be something
 else.

 Here is a tail of the respective log file:

 ##START###
 Initializing Replica Exchange
 Repl  There are 64 replicas:
 Multi-checking the number of atoms ... OK
 Multi-checking the integrator ... OK
 Multi-checking init_step+nsteps ... OK
 Multi-checking first exchange step: init_step/-replex ...
 first exchange step: init_step/-replex is not equal for all subsystems
   subsystem 0: 3062
   subsystem 1: 3062
   subsystem 2: 3062
   subsystem 3: 3062
   subsystem 4: 3062
   subsystem 5: 3062
   subsystem 6: 3062
   subsystem 7: 3062
   subsystem 8: 3062
   subsystem 9: 3062
   subsystem 10: 3062
   subsystem 11: 3062
   subsystem 12: 3062
   subsystem 13: 3062
   subsystem 14: 3062
   subsystem 15: 3062
   subsystem 16: 3062
   subsystem 17: 3062
   subsystem 18: 3062
   subsystem 19: 3062
   subsystem 20: 3062
   subsystem 21: 3062
   subsystem 22: 3062
   subsystem 23: 3062
   subsystem 24: 3062
   subsystem 25: 3062
   subsystem 26: 3062
   subsystem 27: 3062
   subsystem 28: 3062
   subsystem 29: 3062
   subsystem 30: 3062
   subsystem 31: 3062
   subsystem 32: 3062
   subsystem 33: 3062
   subsystem 34: 3062
   subsystem 35: 3062
   subsystem 36: 3062
   subsystem 37: 3062
   subsystem 38: 3062
   subsystem 39: 3066

Seems system 39 got its IO done faster. Its state_prev.cpt will be 3062.
Back up your files. Use gmxcheck to see what's in files. Rename as suitable
so your set of files is consistent.

Mark

   subsystem 40: 3062
   subsystem 41: 3062
   subsystem 42: 3062
   subsystem 43: 3062
   subsystem 44: 3062
   subsystem 45: 3062
   subsystem 46: 3062
   subsystem 47: 3062
   subsystem 48: 3062
   subsystem 49: 3062
   subsystem 50: 3062
   subsystem 51: 3062
   subsystem 52: 3062
   subsystem 53: 3062
   subsystem 54: 3062
   subsystem 55: 3062
   subsystem 56: 3062
   subsystem 57: 3062
   subsystem 58: 3062
   subsystem 59: 3062
   subsystem 60: 3062
   subsystem 61: 3062
   subsystem 62: 3062
   subsystem 63: 3062

 ---
 Program mdrun_mpi, VERSION 4.0.7
 Source code file: main.c, line: 116

 Fatal error:
 The 64 subsystems are not compatible

 ---
 ##END###

 It's clear that init_step/-replex is not equal for all subsystems is the
 problem, but does anyone know why this is happening and how to solve it?

 Thank you for your patience,
 Best regards,

 João Henriques
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Re: [gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L

I think your misunderstanding comes from the belief that sigma (as they are
tabulated in the force field files) should *exactly correspond* to the VDW
diameter, as in encyclopedia.

This is simply not the case. In reality, sigmas in the force fields are
tuned in order to give right interatomic distances AFTER you turn on all
the necessary potentials (Coulombic attraction in case of OPLS).

Dr. Vitaly Chaban





On Mon, Apr 8, 2013 at 3:14 PM, fantasticqhl fantastic...@gmail.com wrote:

  Dear Dr. Vitaly Chaban,

 Thanks very much for concern on my research! We are going to the use the
 bonded model together with Coulomb and LJ potentials.

 My problem is that vdw radius and its sigma do not follow the equation of
 Rvdw = pow(2, 1/6)*sigma in the OPLS force field files,
 not just for copper. That's why I sent these e-mails for suggestions. I am
 sorry for the unclear.

 All the best,
 Qinghua Liao


 On 04/08/2013 01:22 PM, Dr. Vitaly Chaban wrote:

 Dear Qinghua Liao -

  In that case, I am just wishing you luck with the copper containing
 systems.

  Are you going to simulate copper-ligand interactions using Coulomb+LJ
 potential only? I would guess it is a chemical bonding case. Maybe the
 Morse potential (additionally) can be of better service?


  Dr. Vitaly Chaban




 On Mon, Apr 8, 2013 at 1:09 PM, fantasticqhl fantastic...@gmail.comwrote:

  Dear Dr. Vitaly Chaban,

 Thanks very much for your explanation. I guess that I get what you mean
 now! Thanks!

 All the best,
 Qinghua Liao

 On 04/07/2013 11:35 AM, Dr. Vitaly Chaban wrote:

 The equation is a direct consequence of LJ-12-6 equation. This equation
 is used in OPLS and most other force fields.

  The difference you found originate from the fact that, besides LJ
 potential, there is much stronger Coulomb potential in the copper-ion case.
 If you run simulations, you will see that copper-ligand distance is smaller
 than the sum of their sigmas multiplied by pow (2, 1/6).


  Dr. Vitaly Chaban






  On Sun, Apr 7, 2013 at 11:28 AM, fantasticqhl fantastic...@gmail.comwrote:

  Dear Dr. Vitaly Chaban,

 Thanks for the explanation. I know this equation. However, the van der
 Waals radius and its counterpart sigma in OPLS-AA/L force field files do
 not follow this equation.

 For example, the vdw radius of copper ion is 1.4 angstrom, and its sigma
 is  2.08470e-01 (I guess the unit is nm). pow(2, 1/6) is more than 1, so
 obviously this equation
 does not work with copper. So do other atoms. I guess that there might
 be an additional coefficient for this equation in gromacs. That's the
 purpose for asking. Thanks very much!


 All the best,
 Qinghua

 On 04/07/2013 10:48 AM, Dr. Vitaly Chaban wrote:

 Dear Qinghua -

  The formal relation is diameter = pow (2, 1/6) * sigma, provided that
 you have only LJ potential in your interacting subsystem.

  If this is not the case, an optimal sigma can only be found
 iteratively.


  Dr. Vitaly Chaban





 On Sun, Apr 7, 2013 at 10:36 AM, fantasticqhl fantastic...@gmail.comwrote:

 Dear Dr. Vitaly Chaban,

 Thanks very much for your reply. My question is the relationship
 between van der Waals radius and sigma in the OPLS-AA/L force filed files
 of Gromacs.

 Of course I did ab initio optimizations of my system, but I do not know
 there is some relation between the optimal bond length (copper--atom of the
 ligand) and sigma.
 Could you please be more clear and give a little detailed explanation?
 Thanks very much!

 All the best,
 Qinghua

 On 04/06/2013 06:07 PM, Dr. Vitaly Chaban wrote:

 In systems of such kind, everything will depend on the atom of the
 ligand,
 which coordinated by copper ion.

 Perform ab initio geometry optimization and find the optimal distance.
 Then
 adjust sigma(s).

 Dr. Vitaly Chaban







 There is a copper ion with four ligands in my system. I am going to

 study this system using MD simulations.
 For the vdW parameters, R*=1.74 angstrom and epsilon=1.14 kcal.mol
 from
 one paper will be used in our
 simulations. I already found the parameters of copper ion (Cu2+) in
 the
 OPLS-AA/L force field files:
 sigma= 2.08470e-01, epsilon=4.76976e+00, which are for Cu2+ without
 ligands. The two epsilon are the same,
 just with different units.

 My question is that I do not know how to convert the vdW radius to
 sigma. I found that the vdw radius of copper is
 1.4 angstrom, and the sigma in the force field file is 2.08470e-01.
 Could someone tell me how to do the converting?

 Thanks very much!










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Re: [gmx-users] Restarting a REMD simulation (error)

2013-04-08 Thread João Henriques

Thank you very much. I didn't notice it until now considering all those
numbers look so similar. Great eye for detail!

João


On Mon, Apr 8, 2013 at 3:17 PM, Mark Abraham mark.j.abra...@gmail.comwrote:

 On Apr 8, 2013 8:53 AM, João Henriques joao.henriques.32...@gmail.com
 wrote:
 
  Dear all,
 
  Due to cluster wall-time limitations, I was forced to restart two REMD
  simulations. It ran absolutely fine until hitting the wall-time. To
 restart
  I used the following command:
 
  mpirun -np 64 -output-filename MPIoutput $GromDir/mdrun_mpi -s H5_.tpr
  -multi 64 -replex 1000 -deffnm H5_ -cpi -noappend
 
  (I'm using GMX-4.0.7 and yes I know it's old but I have my own reasons
 for
  using it.)
 
  Here is a random replica (#1) MPI output:
 
  ##START###
  NNODES=64, MYRANK=1, HOSTNAME=an091
  NODEID=1 argc=11
  Checkpoint file is from part 1, new output files will be suffixed
 part0002.
  Reading file H5_1.tpr, VERSION 4.0.7 (single precision)
 
  Reading checkpoint file H5_1.cpt generated: Wed Apr  3 17:13:14 2013
 
  ---
  Program mdrun_mpi, VERSION 4.0.7
  Source code file: main.c, line: 116
 
  Fatal error:
  The 64 subsystems are not compatible
 
  ---
 
  Error on node 1, will try to stop all the nodes
  Halting parallel program mdrun_mpi on CPU 1 out of 64
  ##END###
 
  It's reading from the correct cpt and tpr files, so it must be something
  else.
 
  Here is a tail of the respective log file:
 
  ##START###
  Initializing Replica Exchange
  Repl  There are 64 replicas:
  Multi-checking the number of atoms ... OK
  Multi-checking the integrator ... OK
  Multi-checking init_step+nsteps ... OK
  Multi-checking first exchange step: init_step/-replex ...
  first exchange step: init_step/-replex is not equal for all subsystems
subsystem 0: 3062
subsystem 1: 3062
subsystem 2: 3062
subsystem 3: 3062
subsystem 4: 3062
subsystem 5: 3062
subsystem 6: 3062
subsystem 7: 3062
subsystem 8: 3062
subsystem 9: 3062
subsystem 10: 3062
subsystem 11: 3062
subsystem 12: 3062
subsystem 13: 3062
subsystem 14: 3062
subsystem 15: 3062
subsystem 16: 3062
subsystem 17: 3062
subsystem 18: 3062
subsystem 19: 3062
subsystem 20: 3062
subsystem 21: 3062
subsystem 22: 3062
subsystem 23: 3062
subsystem 24: 3062
subsystem 25: 3062
subsystem 26: 3062
subsystem 27: 3062
subsystem 28: 3062
subsystem 29: 3062
subsystem 30: 3062
subsystem 31: 3062
subsystem 32: 3062
subsystem 33: 3062
subsystem 34: 3062
subsystem 35: 3062
subsystem 36: 3062
subsystem 37: 3062
subsystem 38: 3062
subsystem 39: 3066

 Seems system 39 got its IO done faster. Its state_prev.cpt will be 3062.
 Back up your files. Use gmxcheck to see what's in files. Rename as suitable
 so your set of files is consistent.

 Mark

subsystem 40: 3062
subsystem 41: 3062
subsystem 42: 3062
subsystem 43: 3062
subsystem 44: 3062
subsystem 45: 3062
subsystem 46: 3062
subsystem 47: 3062
subsystem 48: 3062
subsystem 49: 3062
subsystem 50: 3062
subsystem 51: 3062
subsystem 52: 3062
subsystem 53: 3062
subsystem 54: 3062
subsystem 55: 3062
subsystem 56: 3062
subsystem 57: 3062
subsystem 58: 3062
subsystem 59: 3062
subsystem 60: 3062
subsystem 61: 3062
subsystem 62: 3062
subsystem 63: 3062
 
  ---
  Program mdrun_mpi, VERSION 4.0.7
  Source code file: main.c, line: 116
 
  Fatal error:
  The 64 subsystems are not compatible
 
  ---
  ##END###
 
  It's clear that init_step/-replex is not equal for all subsystems is
 the
  problem, but does anyone know why this is happening and how to solve it?
 
  Thank you for your patience,
  Best regards,
 
  João Henriques
  --
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  http://lists.gromacs.org/mailman/listinfo/gmx-users
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 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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João Henriques
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Re: [gmx-users] Calculation of Temperature of Cluster

Justin,
Thanks for your comment.

Instead of .xtc, I just used .trr in which nstvout isn’t zero. I'm still
encountering to empty file for temperature.

Rasoul


On Mon, Apr 8, 2013 at 2:10 PM, Justin Lemkul jalem...@vt.edu wrote:

 On Mon, Apr 8, 2013 at 9:08 AM, Rasoul Nasiri nasiri1...@gmail.com
 wrote:

  Bellow is my command which I used:
 
  g_clustsize_d -f traj.xtc  -s topol.tpr -n n.ndx -nc nclust.xvg -mc
  maxclust
  .xvg -ac avclust.xvg -mcn maxclust.ndx -cut 0.516 -temp Tempe.xvg
 
 
 Then it is exactly what I said. Temperatures require velocities. Velocities
 are not stored in .xtc files and thus you can't extract any temperature
 information in this way.

 -Justin

 --

 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540)
 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
 --
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 http://lists.gromacs.org/mailman/listinfo/gmx-users
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 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] Calculation of Temperature of Cluster

On Mon, Apr 8, 2013 at 9:24 AM, Rasoul Nasiri nasiri1...@gmail.com wrote:

 Justin,
 Thanks for your comment.

 Instead of .xtc, I just used .trr in which nstvout isn’t zero. I'm still
 encountering to empty file for temperature.


Can you please provide the gmxcheck output for the .trr file? I suppose
there could be a bug, but we need to rule out a few things first. If
g_clustsize still fails, you can get the output temperature from g_traj
-ot, which appears to have a redundant function.

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L

2013-04-08 Thread fantasticqhl


Dear Dr. Vitaly Chaban,

Thanks very much for your patient explanation. Yeah, you are right, that 
is what I want to know: how you tuned this parameter?


Since then, if I want to set a new atom type and I know its vdw radius, 
so how should I set the sigma for it based on the vdw radius,
which should be in agreement with OPLS-AA/L force filed? Could you give 
me some suggestions?
I guess that I have to tune it by myself this time, right? Thanks in 
advance!


All the best,
Qinghua Liao




On 04/08/2013 03:21 PM, Dr. Vitaly Chaban wrote:
I think your misunderstanding comes from the belief that sigma (as 
they are tabulated in the force field files) should *exactly 
correspond* to the VDW diameter, as in encyclopedia.


This is simply not the case. In reality, sigmas in the force fields 
are tuned in order to give right interatomic distances AFTER you 
turn on all the necessary potentials (Coulombic attraction in case of 
OPLS).


Dr. Vitaly Chaban





On Mon, Apr 8, 2013 at 3:14 PM, fantasticqhl fantastic...@gmail.com 
mailto:fantastic...@gmail.com wrote:


Dear Dr. Vitaly Chaban,

Thanks very much for concern on my research! We are going to the
use the bonded model together with Coulomb and LJ potentials.

My problem is that vdw radius and its sigma do not follow the
equation of  Rvdw = pow(2, 1/6)*sigma in the OPLS force field files,
not just for copper. That's why I sent these e-mails for
suggestions. I am sorry for the unclear.

All the best,
Qinghua Liao


On 04/08/2013 01:22 PM, Dr. Vitaly Chaban wrote:

Dear Qinghua Liao -

In that case, I am just wishing you luck with the copper
containing systems.

Are you going to simulate copper-ligand interactions using
Coulomb+LJ potential only? I would guess it is a chemical bonding
case. Maybe the Morse potential (additionally) can be of better
service?


Dr. Vitaly Chaban




On Mon, Apr 8, 2013 at 1:09 PM, fantasticqhl
fantastic...@gmail.com mailto:fantastic...@gmail.com wrote:

Dear Dr. Vitaly Chaban,

Thanks very much for your explanation. I guess that I get
what you mean now! Thanks!

All the best,
Qinghua Liao

On 04/07/2013 11:35 AM, Dr. Vitaly Chaban wrote:

The equation is a direct consequence of LJ-12-6 equation.
This equation is used in OPLS and most other force fields.

The difference you found originate from the fact that,
besides LJ potential, there is much stronger Coulomb
potential in the copper-ion case. If you run simulations,
you will see that copper-ligand distance is smaller than the
sum of their sigmas multiplied by pow (2, 1/6).


Dr. Vitaly Chaban






On Sun, Apr 7, 2013 at 11:28 AM, fantasticqhl
fantastic...@gmail.com mailto:fantastic...@gmail.com wrote:

Dear Dr. Vitaly Chaban,

Thanks for the explanation. I know this equation.
However, the van der Waals radius and its counterpart
sigma in OPLS-AA/L force field files do not follow this
equation.

For example, the vdw radius of copper ion is 1.4
angstrom, and its sigma is  2.08470e-01 (I guess the
unit is nm). pow(2, 1/6) is more than 1, so obviously
this equation
does not work with copper. So do other atoms. I guess
that there might be an additional coefficient for this
equation in gromacs. That's the purpose for asking.
Thanks very much!


All the best,
Qinghua

On 04/07/2013 10:48 AM, Dr. Vitaly Chaban wrote:

Dear Qinghua -

The formal relation is diameter = pow (2, 1/6) * sigma,
provided that you have only LJ potential in your
interacting subsystem.

If this is not the case, an optimal sigma can only be
found iteratively.


Dr. Vitaly Chaban





On Sun, Apr 7, 2013 at 10:36 AM, fantasticqhl
fantastic...@gmail.com
mailto:fantastic...@gmail.com wrote:

Dear Dr. Vitaly Chaban,

Thanks very much for your reply. My question is the
relationship between van der Waals radius and sigma
in the OPLS-AA/L force filed files of Gromacs.

Of course I did ab initio optimizations of my
system, but I do not know there is some relation
between the optimal bond length (copper--atom of
the ligand) and sigma.
Could you please be more clear and give a little
detailed explanation? Thanks very much!

All the best,
Qinghua

On 04/06/2013 06:07 PM, Dr. Vitaly Chaban wrote:

In systems of such kind, everything will depend
on the atom of the

Re: [gmx-users] Calculation of Temperature of Cluster

One suggestion,

Is there any chance to retrieve trajectory of un-evaporated molecules using
one of gromacs tools? Now I have a ndx file which show number of atoms
stayed in drop,

Which one is better? I mean if I can get trajectory (position+velocity)
unevaporated molecules, I would be able estimate the temperature as well.
Is it correct?

Rasoul


On Mon, Apr 8, 2013 at 2:30 PM, Justin Lemkul jalem...@vt.edu wrote:

 On Mon, Apr 8, 2013 at 9:24 AM, Rasoul Nasiri nasiri1...@gmail.com
 wrote:

  Justin,
  Thanks for your comment.
 
  Instead of .xtc, I just used .trr in which nstvout isn’t zero. I'm still
  encountering to empty file for temperature.
 
 
 Can you please provide the gmxcheck output for the .trr file? I suppose
 there could be a bug, but we need to rule out a few things first. If
 g_clustsize still fails, you can get the output temperature from g_traj
 -ot, which appears to have a redundant function.

 -Justin

 --

 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540)
 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 * Please don't post (un)subscribe requests to the list. Use the
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Re: [gmx-users] Calculation of Temperature of Cluster

On Mon, Apr 8, 2013 at 9:39 AM, Rasoul Nasiri nasiri1...@gmail.com wrote:

 One suggestion,

 Is there any chance to retrieve trajectory of un-evaporated molecules using
 one of gromacs tools? Now I have a ndx file which show number of atoms
 stayed in drop,


Sure, that's what trjconv does.


 Which one is better? I mean if I can get trajectory (position+velocity)
 unevaporated molecules, I would be able estimate the temperature as well.
 Is it correct?


I suppose so. You can (in theory) use g_traj or g_clustsize to extract
temperature, and the analyzed atoms can be chosen as an index group of a
larger system or simply that subset that has already been parsed out of the
trajetory. Either approach should be equivalent.

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


-- 
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Re: [gmx-users] Improve performance

These are almost irrelevant for performance. What are you actually
simulating on what?

Mark
On Apr 7, 2013 2:12 AM, 陈照云 chenzhaoyu...@gmail.com wrote:

 Hi!
 I have 6 nodes. Each node has two CPUs,12 cores totally.
 How should I set the options like -rdd,-rcon,-dds,-gcom to improve the
 performance?
 Thanks!
 --
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Aw: [gmx-users] Re: Simulating a large system

2013-04-08 Thread lloyd riggs

Funny, I thought of a large Ribosome system. You can in vacuo already with an i7 or AMD equivalent EM a 600 amino acid system with a 12-15A solvent shell in an hour to three using the CPU alone. Thats from test of Gromacs and a non-eqd system. so about 1 work day to get through NPT. Thus, I doubt there is much problem even using the whole system for most things if your time frame is a day or two and newer PC .

Stephan Watkins

Gesendet:Montag, 08. April 2013 um 11:35 Uhr
Von:Juan Antonio Raygoza Garay raygo...@psu.edu
An:vvcha...@gmail.com
Cc:gmx-users@gromacs.org
Betreff:[gmx-users] Re: Simulating a large system

Sure, its basically improving minimization time. if i can focus all my resources in simulating or minimizing a portion of the system while ignoring other parts that are too far away from the selected portion, it can also be possible to run some simulations without the need of a big cluster and sort of obtaining about the same results. This goes to my interest of harnessing small computing systems for doing all these tasks. There are systems like rna molecules where i could get the fine grained structure first and then running the entire molecule to obtain the coarser structure.

As someone says it might not improve time but at least having the ability to run portions only on my small desktop overnight or just leave it there running a lot of this could be accomplished. I do have access to a cluster but having to wait in the queue is time that can be used to getting somewhere, maybe slower but youre moving.

On Apr 8, 2013, at 5:20 AM, Dr. Vitaly Chaban wrote:

Vitaly Chaban

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Re: [gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L

On Mon, Apr 8, 2013 at 3:36 PM, fantasticqhl fantastic...@gmail.com wrote:

  Dear Dr. Vitaly Chaban,

 Thanks very much for your patient explanation. Yeah, you are right, that
 is what I want to know: how you tuned this parameter?

 Since then, if I want to set a new atom type and I know its vdw radius, so
 how should I set the sigma for it based on the vdw radius,



You cannot set the sigma based ONLY on the VDW radius.



  which should be in agreement with OPLS-AA/L force filed? Could you give
 me some suggestions?
 I guess that I have to tune it by myself this time, right? Thanks in
 advance!



I would do the following:

1) Optimize ion-ligand complex using ab initio. Write down binding energy
and optimal distance;
2) Construct topology for classical MD using approximate sigma;
3) Calculate energy and distance from classical MD;
4) Compare them to distance and energy from ab initio;
5) If you are not satisfied, adjust your sigma;
6) Repeat classical MD until the difference between ion-ligand distance in
classical MD becomes reasonably similar to that in ab initio.

To preserve compatibility with OPLS, use the same level of theory in ab
initio, which they used when derived OPLS. Keep in mind that their original
level of theory is not so perfect...


Dr. Vitaly Chaban




 All the best,
 Qinghua Liao




 On 04/08/2013 03:21 PM, Dr. Vitaly Chaban wrote:

 I think your misunderstanding comes from the belief that sigma (as they
 are tabulated in the force field files) should *exactly correspond* to the
 VDW diameter, as in encyclopedia.

  This is simply not the case. In reality, sigmas in the force fields are
 tuned in order to give right interatomic distances AFTER you turn on all
 the necessary potentials (Coulombic attraction in case of OPLS).

  Dr. Vitaly Chaban





 On Mon, Apr 8, 2013 at 3:14 PM, fantasticqhl fantastic...@gmail.comwrote:

  Dear Dr. Vitaly Chaban,

 Thanks very much for concern on my research! We are going to the use the
 bonded model together with Coulomb and LJ potentials.

 My problem is that vdw radius and its sigma do not follow the equation
 of  Rvdw = pow(2, 1/6)*sigma in the OPLS force field files,
 not just for copper. That's why I sent these e-mails for suggestions. I
 am sorry for the unclear.

 All the best,
 Qinghua Liao


 On 04/08/2013 01:22 PM, Dr. Vitaly Chaban wrote:

 Dear Qinghua Liao -

  In that case, I am just wishing you luck with the copper containing
 systems.

  Are you going to simulate copper-ligand interactions using Coulomb+LJ
 potential only? I would guess it is a chemical bonding case. Maybe the
 Morse potential (additionally) can be of better service?


  Dr. Vitaly Chaban




 On Mon, Apr 8, 2013 at 1:09 PM, fantasticqhl fantastic...@gmail.comwrote:

  Dear Dr. Vitaly Chaban,

 Thanks very much for your explanation. I guess that I get what you mean
 now! Thanks!

 All the best,
 Qinghua Liao

 On 04/07/2013 11:35 AM, Dr. Vitaly Chaban wrote:

 The equation is a direct consequence of LJ-12-6 equation. This equation
 is used in OPLS and most other force fields.

  The difference you found originate from the fact that, besides LJ
 potential, there is much stronger Coulomb potential in the copper-ion case.
 If you run simulations, you will see that copper-ligand distance is smaller
 than the sum of their sigmas multiplied by pow (2, 1/6).


  Dr. Vitaly Chaban






  On Sun, Apr 7, 2013 at 11:28 AM, fantasticqhl 
 fantastic...@gmail.comwrote:

  Dear Dr. Vitaly Chaban,

 Thanks for the explanation. I know this equation. However, the van der
 Waals radius and its counterpart sigma in OPLS-AA/L force field files do
 not follow this equation.

 For example, the vdw radius of copper ion is 1.4 angstrom, and its
 sigma is  2.08470e-01 (I guess the unit is nm). pow(2, 1/6) is more than 1,
 so obviously this equation
 does not work with copper. So do other atoms. I guess that there might
 be an additional coefficient for this equation in gromacs. That's the
 purpose for asking. Thanks very much!


 All the best,
 Qinghua

 On 04/07/2013 10:48 AM, Dr. Vitaly Chaban wrote:

 Dear Qinghua -

  The formal relation is diameter = pow (2, 1/6) * sigma, provided that
 you have only LJ potential in your interacting subsystem.

  If this is not the case, an optimal sigma can only be found
 iteratively.


  Dr. Vitaly Chaban





 On Sun, Apr 7, 2013 at 10:36 AM, fantasticqhl 
 fantastic...@gmail.comwrote:

 Dear Dr. Vitaly Chaban,

 Thanks very much for your reply. My question is the relationship
 between van der Waals radius and sigma in the OPLS-AA/L force filed files
 of Gromacs.

 Of course I did ab initio optimizations of my system, but I do not
 know there is some relation between the optimal bond length (copper--atom
 of the ligand) and sigma.
 Could you please be more clear and give a little detailed explanation?
 Thanks very much!

 All the best,
 Qinghua

 On 04/06/2013 06:07 PM, Dr. Vitaly Chaban wrote:

 In systems of such kind, everything will

Re: [gmx-users] GROMACS 4.6v - Myrinet2000

2013-04-08 Thread Szilárd Páll

On Mon, Apr 8, 2013 at 1:37 PM, Justin Lemkul jalem...@vt.edu wrote:

 On Mon, Apr 8, 2013 at 2:28 AM, Hrachya Astsatryan hr...@sci.am wrote:

  Dear all,
 
  We have installed the latest version of Gromacs (version 4.6) on our
  cluster by the following step:
 
   * cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/**backup/sicnas/gromacs
 -DGMX_BUILD_OWN_FFTW=ON -DGMX_PREFER_STATIC_LIBS=ON
 
 
 With this command, you're building Gromacs' internal FFT rather than using
 FFTW. Your performance will be much better if you use FFTW. See the
 installation instructions for more information.


No, the GMX_BUILD_OWN_FFTW option will simply tell the build system to
download FFTW 3.3(.3?), build it, and link it statically against mdrun. I'm
just realizing that the naming of the option allows it to be confused with
GROMACS' built-in (=own) fftpack (which is typically at 2-3x+ slower).

Unfortunately, the install guide refers to the option as
-DGMX_BUILD_OWN_FFTW=ON which means that even Google can't find it.

http://www.gromacs.org/Documentation/Installation_Instructions#3.4.1._FFTW

Cheers,
--
Szilard



 -Justin


  The interconnection of the cluster is Myrinet2000 and the driver is MX
  (and mpich 1.3.1).
 
  The job scripts (see below) and different simulations show that there is
  no adequate performance (usually it should be 2-3 time more).
 
  Could you, pls. help us to overcome the problem in order to get better
  performance?
 
  With regards,
  Hrach
 
  #PBS -l nodes=8:ppn=2
  ##PBS -l walltime=360:00
  #PBS -q armcluster
  #PBS -e 33mM_16_new.err
  #PBS -o 33mM_16_new.log
  ## Specify the shell to be bash
  #PBS -S /bin/bash
 
  export LD_LIBRARY_PATH=$LD_LIBRARY_**PATH:/backup/sicnas/gromacs/**
  lib:/opt/mpi/lib
 
  /opt/mpi/bin/mpirun -machinefile /backup/sicnas/npt101/machine -np 16
  /backup/sicnas/gromacs/bin/**mdrun_mpi -s
 /backup/sicnas/npt101/topol.**tpr
  -v
 
 
 
 
 
  --
  Hrachya Astsatryan
  Head of HPC Laboratory,
  Institute for Informatics and Automation Problems,
  National Academy of Sciences of the Republic of Armenia
  1, P. Sevak str., Yerevan 0014, Armenia
  t: 374 10 284780
  f: 374 10 285812
  e: hr...@sci.am
  skype: tighra
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 --

 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540)
 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 
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[gmx-users] Quadro FX 5800 incompatible?

2013-04-08 Thread bv07ay

I have recently installed version 4.6.1. The installation was successful with
all of the prerequisites, however mdrun tells me that the Quadro FX 5800 is
incompatible even though it is listed on the site as compatible. 


1 GPU detected: 
  #0: NVIDIA Quadro FX 5800, compute cap.: 1.3, ECC:  no, stat: incompatible 



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Re: [gmx-users] Quadro FX 5800 incompatible?

On Mon, Apr 8, 2013 at 10:40 AM, bv07ay bv0...@brocku.ca wrote:

 I have recently installed version 4.6.1. The installation was successful
 with
 all of the prerequisites, however mdrun tells me that the Quadro FX 5800 is
 incompatible even though it is listed on the site as compatible.


 1 GPU detected:
   #0: NVIDIA Quadro FX 5800, compute cap.: 1.3, ECC:  no, stat:
 incompatible


The GPU site on gromacs.org is wildly outdated and refers only to OpenMM
features. For native GPU acceleration in Gromacs 4.6.x, you need a GPU with
compute capability = 2.0.

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_hbond

2013-04-08 Thread Nilesh Dhumal

Hello,

I am calculating the hydrogen bond life time for my system, ionic liquids.

I am calculating the hydrogen bond life time using g_hbond in Groamcs.

Attached the plot p(t)vs time and the exponential decay is not sooth.

Can you tell why is there is lot of noise.

Nilesh



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Re: [gmx-users] Re: RDF output has no data

2013-04-08 Thread Venkat Reddy

Sir

I loaded the trajectory. There doesn't seem to be anything wrong with it.
Have no clue whats going wrong

Thanks


On Mon, Apr 8, 2013 at 5:28 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:

 I believe the problem is in the way which you used to convert AMBER
 trajectory to the GROMACS trajectory

 I would suggest to try gmxdump and see what your trajectory looks like. Oe
 maybe even better - try to visualize it in VMD to see if the format is
 correct.

 Dr. Vitaly Chaban



 Sir
 
  I was using an old version. Now I used 4.5.5, it still gives me the same
  blank output file.
 
  Kindly suggest how to go about solving this
 
  Thanks
 
 
  On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham mark.j.abra...@gmail.com
  wrote:
 
   On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy venkat...@gmail.com
  wrote:
  
There was no fatal error preceding the output. After selecting the
  groups
following are the output on the screen
Reading frame   1 time0.100
Warning: can not make broken molecules whole without a run input
 file,
 don't worry, mdrun doesn't write broken molecules
   
  
   This message is from a prehistoric version of g_rdf. Please get a new
  one.
  
   Mark
  
  
   
Reading frame2000 time  200.000
   
   
gcq#69: The Wheels On the Bus Go Round and Round (J. Richman)
   
And the rdf.xvg file looks like this
   
#This file was created Sat Apr  6 10:54:13 2013
# by the following command:
# g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg
#
# g_rdf is part of G R O M A C S:
#
# GROningen MAchine for Chemical Simulation
#
@title Radial Distribution
@xaxis  label r
@yaxis  label 
@TYPE xy
@ subtitle O21-H2__CAT
 0.001  1
~
   
Whats going wrong? Please help.
 
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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] Re: RDF output has no data

Do you experience this problem with g_rdf only, or with all gromacs
analysis utilities?


On Mon, Apr 8, 2013 at 7:33 PM, Venkat Reddy venkat...@gmail.com wrote:

 Sir

 I loaded the trajectory. There doesn't seem to be anything wrong with it.
 Have no clue whats going wrong

 Thanks


 On Mon, Apr 8, 2013 at 5:28 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:

 I believe the problem is in the way which you used to convert AMBER
 trajectory to the GROMACS trajectory

 I would suggest to try gmxdump and see what your trajectory looks like. Oe
 maybe even better - try to visualize it in VMD to see if the format is
 correct.

 Dr. Vitaly Chaban



 Sir
 
  I was using an old version. Now I used 4.5.5, it still gives me the same
  blank output file.
 
  Kindly suggest how to go about solving this
 
  Thanks
 
 
  On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham mark.j.abra...@gmail.com
  wrote:
 
   On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy venkat...@gmail.com
  wrote:
  
There was no fatal error preceding the output. After selecting the
  groups
following are the output on the screen
Reading frame   1 time0.100
Warning: can not make broken molecules whole without a run input
 file,
 don't worry, mdrun doesn't write broken molecules
   
  
   This message is from a prehistoric version of g_rdf. Please get a new
  one.
  
   Mark
  
  
   
Reading frame2000 time  200.000
   
   
gcq#69: The Wheels On the Bus Go Round and Round (J. Richman)
   
And the rdf.xvg file looks like this
   
#This file was created Sat Apr  6 10:54:13 2013
# by the following command:
# g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg
#
# g_rdf is part of G R O M A C S:
#
# GROningen MAchine for Chemical Simulation
#
@title Radial Distribution
@xaxis  label r
@yaxis  label 
@TYPE xy
@ subtitle O21-H2__CAT
 0.001  1
~
   
Whats going wrong? Please help.
 
 --
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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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[gmx-users] can I change atom position after x steps

2013-04-08 Thread fatemeh ramezani

Dear all

 I am simulating gold nanoparticle interaction with 10 aminoacids.Two amino 
acids have been far from the nanoparticleafter 2000 steps. 
Now, Can I change after2000 steps, the position of these 2 aminoacids in  PDP 
file and then continue the simulation?


Fatemeh Ramezani
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Re: [gmx-users] can I change atom position after x steps

On Mon, Apr 8, 2013 at 2:00 PM, fatemeh ramezani fr_...@yahoo.com wrote:

 Dear all

  I am simulating gold nanoparticle interaction with 10 aminoacids.Two
 amino acids have been far from the nanoparticleafter 2000 steps.
 Now, Can I change after2000 steps, the position of these 2 aminoacids in
 PDP file and then continue the simulation?


I doubt that would be stable. You've taken a trajectory that has run for
some amount of time, seriously perturbed it, then you hope to continue it?
 You're better off starting a new simulation altogether. Also realize that
2000 steps, irrespective of what the timestep is, is extremely short.

-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Restarting a REMD simulation (error)

It helped that I *really* knew one must differ ;-)

Mark
On Apr 8, 2013 2:24 PM, João Henriques joao.henriques.32...@gmail.com
wrote:

 Thank you very much. I didn't notice it until now considering all those
 numbers look so similar. Great eye for detail!

 João


 On Mon, Apr 8, 2013 at 3:17 PM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

  On Apr 8, 2013 8:53 AM, João Henriques joao.henriques.32...@gmail.com
 
  wrote:
  
   Dear all,
  
   Due to cluster wall-time limitations, I was forced to restart two REMD
   simulations. It ran absolutely fine until hitting the wall-time. To
  restart
   I used the following command:
  
   mpirun -np 64 -output-filename MPIoutput $GromDir/mdrun_mpi -s H5_.tpr
   -multi 64 -replex 1000 -deffnm H5_ -cpi -noappend
  
   (I'm using GMX-4.0.7 and yes I know it's old but I have my own reasons
  for
   using it.)
  
   Here is a random replica (#1) MPI output:
  
   ##START###
   NNODES=64, MYRANK=1, HOSTNAME=an091
   NODEID=1 argc=11
   Checkpoint file is from part 1, new output files will be suffixed
  part0002.
   Reading file H5_1.tpr, VERSION 4.0.7 (single precision)
  
   Reading checkpoint file H5_1.cpt generated: Wed Apr  3 17:13:14 2013
  
   ---
   Program mdrun_mpi, VERSION 4.0.7
   Source code file: main.c, line: 116
  
   Fatal error:
   The 64 subsystems are not compatible
  
   ---
  
   Error on node 1, will try to stop all the nodes
   Halting parallel program mdrun_mpi on CPU 1 out of 64
   ##END###
  
   It's reading from the correct cpt and tpr files, so it must be
 something
   else.
  
   Here is a tail of the respective log file:
  
   ##START###
   Initializing Replica Exchange
   Repl  There are 64 replicas:
   Multi-checking the number of atoms ... OK
   Multi-checking the integrator ... OK
   Multi-checking init_step+nsteps ... OK
   Multi-checking first exchange step: init_step/-replex ...
   first exchange step: init_step/-replex is not equal for all subsystems
 subsystem 0: 3062
 subsystem 1: 3062
 subsystem 2: 3062
 subsystem 3: 3062
 subsystem 4: 3062
 subsystem 5: 3062
 subsystem 6: 3062
 subsystem 7: 3062
 subsystem 8: 3062
 subsystem 9: 3062
 subsystem 10: 3062
 subsystem 11: 3062
 subsystem 12: 3062
 subsystem 13: 3062
 subsystem 14: 3062
 subsystem 15: 3062
 subsystem 16: 3062
 subsystem 17: 3062
 subsystem 18: 3062
 subsystem 19: 3062
 subsystem 20: 3062
 subsystem 21: 3062
 subsystem 22: 3062
 subsystem 23: 3062
 subsystem 24: 3062
 subsystem 25: 3062
 subsystem 26: 3062
 subsystem 27: 3062
 subsystem 28: 3062
 subsystem 29: 3062
 subsystem 30: 3062
 subsystem 31: 3062
 subsystem 32: 3062
 subsystem 33: 3062
 subsystem 34: 3062
 subsystem 35: 3062
 subsystem 36: 3062
 subsystem 37: 3062
 subsystem 38: 3062
 subsystem 39: 3066
 
  Seems system 39 got its IO done faster. Its state_prev.cpt will be 3062.
  Back up your files. Use gmxcheck to see what's in files. Rename as
 suitable
  so your set of files is consistent.
 
  Mark
 
 subsystem 40: 3062
 subsystem 41: 3062
 subsystem 42: 3062
 subsystem 43: 3062
 subsystem 44: 3062
 subsystem 45: 3062
 subsystem 46: 3062
 subsystem 47: 3062
 subsystem 48: 3062
 subsystem 49: 3062
 subsystem 50: 3062
 subsystem 51: 3062
 subsystem 52: 3062
 subsystem 53: 3062
 subsystem 54: 3062
 subsystem 55: 3062
 subsystem 56: 3062
 subsystem 57: 3062
 subsystem 58: 3062
 subsystem 59: 3062
 subsystem 60: 3062
 subsystem 61: 3062
 subsystem 62: 3062
 subsystem 63: 3062
  
   ---
   Program mdrun_mpi, VERSION 4.0.7
   Source code file: main.c, line: 116
  
   Fatal error:
   The 64 subsystems are not compatible
  
   ---
   ##END###
  
   It's clear that init_step/-replex is not equal for all subsystems is
  the
   problem, but does anyone know why this is happening and how to solve
 it?
  
   Thank you for your patience,
   Best regards,
  
   João Henriques
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Aw: Re: [gmx-users] MD publications

2013-04-08 Thread lloyd riggs


Sorry, I tried posting this once but it was spammed or something. In any case, are there any suggestions for mostly MD based journals (publication wise as content), a favorites or something if somone wanted to turn it into that,



Stephan Watkins
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[gmx-users] installing CGenFF in Gromacs

2013-04-08 Thread jbermudez

Hi!

I'm interested in using CHARMM's General Force Field for organic molecules
(CGenFF) in Gromacs.

For that, I've downloaded the files top_all36_cgenff.rtf,
par_all36_cgenff.prm (from http://mackerell.umaryland.edu/~kenno/cgenff/)
which, correspond to the topology and parameters files respectively (both
files in CHARMM native formats).

Are these the correct files to install the CGenFF?
Should I do something with these files to be readable by Gromacs?
Where should I place these files in order get them installed?

I would appreciate any guidance or correction if I'm misinterpreting
something.

Thanks in advance!



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Re: [gmx-users] installing CGenFF in Gromacs

On Mon, Apr 8, 2013 at 7:56 PM, jbermudez bto89meis...@gmail.com wrote:

 Hi!

 I'm interested in using CHARMM's General Force Field for organic molecules
 (CGenFF) in Gromacs.

 For that, I've downloaded the files top_all36_cgenff.rtf,
 par_all36_cgenff.prm (from http://mackerell.umaryland.edu/~kenno/cgenff/)
 which, correspond to the topology and parameters files respectively (both
 files in CHARMM native formats).

 Are these the correct files to install the CGenFF?
 Should I do something with these files to be readable by Gromacs?
 Where should I place these files in order get them installed?

 I would appreciate any guidance or correction if I'm misinterpreting
 something.


Start with Chapter 5 of the manual for details of force field organization
and required file format. Files in CHARMM format are going to be completely
useless in Gromacs. Various scripts exist around the web to convert
formats, though most are old and may not work entirely correctly.

-Justin

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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] About k20

2013-04-08 Thread 陈照云

Hi!
   I want to improve my mdrun performance with k20.But there is something
wrong.
  My gromacs version is 4.6.1. My openmm version is 5.0.1. The wrong
message is include could not find load file:  ../contrib/BuildMdrunOpenMM
   Can the openmm version match k20?
  Thanks!
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Re: [gmx-users] About k20