date:20130408

So there is a problem with your trajectory file. Try to understand what
kind of problem it is.

I can recollect that I experienced something like that why translating CPMD
trajectory to GROMACS. Maybe, it does not write time for each frame at the
right place -- just a guess.

Dr. Vitaly Chaban




On Tue, Apr 9, 2013 at 7:44 AM, Venkat Reddy  wrote:

> Sir
>
> I tried g_msd, after asking for group selection the program appears not to
> read the frames as it remains stuck at reading frame 0, time 0.00.
>
> What to do?
>
> Thanks
>
>
>
>
> On Mon, Apr 8, 2013 at 11:16 PM, Dr. Vitaly Chaban wrote:
>
>> 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  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 wrote:
>>>
 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 
 > 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.
 >
 --
 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!
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>>>
>>>
>>>
>>> --
>>> 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] doubt in remd

2013-04-08 Thread Shine A

Respected sir,

I successfully  completed REMD simulation. Now I am
struggling with analysis part. Here how I select the global minimum  from
replica? Can you give some suggestions about the analysis part?
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[gmx-users] Obtain frames from every one ps

2013-04-08 Thread Ashalatha Sreshty

Dear All,

I need help in obtaining frames from every one ps of a trajectory. My
problem is as described:

I obtained a 100ns trajectory, I get one frame for every 5 ps from my
initial, but my new trajectory is generated by catenating different frames
that fall in the bins of PCA space of the first two PC components with
lowest energy. Now that, I want to do the analysis like angle average, RMSD
etc on all the frames, I would like to know how to obtain frames from this
new trajectory at every one ps.

Please help me. Thanks in advance.

Dr. Asha Latha Sreshty,
Post Doctoral Fellow,
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore - 560012
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Re: [gmx-users] Re: RDF output has no data

2013-04-08 Thread Venkat Reddy

Sir

I tried g_msd, after asking for group selection the program appears not to
read the frames as it remains stuck at reading frame 0, time 0.00.

What to do?

Thanks




On Mon, Apr 8, 2013 at 11:16 PM, Dr. Vitaly Chaban wrote:

> 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  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 wrote:
>>
>>> 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 >> > >wrote:
>>> >
>>> > > On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy 
>>> > 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.
>>> >
>>> --
>>> 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!
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>>> www interface or send it 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
>>
>
>


-- 
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] About k20

On Mon, Apr 8, 2013 at 8:58 PM, 陈照云  wrote:

> 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?
>

OpenMM is barely supported, and probably doesn't even build right in
version 4.6.1. Note that OpenMM was only needed in the 4.5.x series for
GPU-compatible implicit solvent calculations. Version 4.6 introduced native
GPU support for explicit-solvent simulations. You still need OpenMM for
implicit-solvent simulations, but I would be very surprised if it even
built. There is some work going on in the development branch to fix OpenMM
support, but in the long run, it will be completely dropped in favor of
native Gromacs code.

-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] 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] installing CGenFF in Gromacs

On Mon, Apr 8, 2013 at 7:56 PM, jbermudez  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

-- 



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] 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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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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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" 
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  >wrote:
>
> > On Apr 8, 2013 8:53 AM, "João Henriques"  >
> > 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
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
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> > > www interface

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

On Mon, Apr 8, 2013 at 2:00 PM, fatemeh ramezani  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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[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] 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  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 wrote:
>
>> 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 > > >wrote:
>> >
>> > > On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy 
>> > 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.
>> >
>> --
>> 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!
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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

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 wrote:

> 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  > >wrote:
> >
> > > On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy 
> > 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.
> >
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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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] 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] Quadro FX 5800 incompatible?

On Mon, Apr 8, 2013 at 10:40 AM, bv07ay  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] 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] GROMACS 4.6v - Myrinet2000

2013-04-08 Thread Szilárd Páll

On Mon, Apr 8, 2013 at 1:37 PM, Justin Lemkul  wrote:

> On Mon, Apr 8, 2013 at 2:28 AM, Hrachya Astsatryan  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
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > * Please search the archive at http://www.gromacs.org/**
> > Support/Mailing_Lists/Search<
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> http://www.gromacs.org/Support/Mailing_Lists>
> >
>
>
>
> --
>
> 
>
> 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

On Mon, Apr 8, 2013 at 3:36 PM, fantasticqhl  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 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 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 
>>> 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 
 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 optima

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-eq'd 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"
An: vvcha...@gmail.com
Cc: gmx-users@gromacs.org
Betreff: [gmx-users] Re: Simulating a large system

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

On Mon, Apr 8, 2013 at 9:39 AM, Rasoul Nasiri  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] 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  wrote:

> On Mon, Apr 8, 2013 at 9:24 AM, Rasoul Nasiri 
> 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!
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>
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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 > 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
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
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
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

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

On Mon, Apr 8, 2013 at 9:24 AM, Rasoul Nasiri  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] 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  wrote:

> On Mon, Apr 8, 2013 at 9:08 AM, Rasoul Nasiri 
> 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
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
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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 wrote:

> On Apr 8, 2013 8:53 AM, "João Henriques" 
> 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
> > --
> > 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!
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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  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 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 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 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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http://lists.gromacs.org/mail

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

On Apr 8, 2013 8:53 AM, "João Henriques" 
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
> --
> 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] 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 > 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
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
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] amber99 with berger's lipids

On Mon, Apr 8, 2013 at 7:50 AM, James Starlight wrote:

> 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

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Department of Biochemistry
Virginia Tech
Blacksburg, VA
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Re: [gmx-users] Calculation of Temperature of Cluster

On Mon, Apr 8, 2013 at 9:08 AM, Rasoul Nasiri  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

-- 



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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

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  wrote:

> On Mon, Apr 8, 2013 at 9:01 AM, Rasoul Nasiri 
> 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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> >
>
>
>
> --
>
> 
>
> 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] Calculation of Temperature of Cluster

On Mon, Apr 8, 2013 at 9:01 AM, Rasoul Nasiri  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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-- 



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] 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"  wrote:

> On Mon, Apr 8, 2013 at 5:54 AM, Dr. Vitaly Chaban  >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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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" 
wrote:

> Hi, is it possible to instruct gromacs to only perform the dynamics on
> half of the system or protein while ignoring the rest?
>
> thanks--
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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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[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  >wrote:
>
> > On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy 
> 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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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 

> On Sat, Apr 6, 2013 at 10:46 AM, Albert  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
>
> --
>
> 
>
> 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: Simulating a large system

On Mon, Apr 8, 2013 at 5:54 AM, Dr. Vitaly Chaban 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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Re: [gmx-users] MD with Xenon

2013-04-08 Thread Anirban

On Mon, Apr 8, 2013 at 5:04 PM, Divya Sunil wrote:

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

On Mon, Apr 8, 2013 at 2:28 AM, Hrachya Astsatryan  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
>
>
>
>
>
> --
> 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
> --
> 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/Searchbefore
>  posting!
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> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
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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] 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] 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  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 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 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] 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 wrote:

> On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy  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  wrote:
> >
> > > On Fri, Apr 5, 2013 at 2:30 PM, Venkat Reddy 
> > 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
> > >
> > > 
> > > --
> > > 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!
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> > > www interface or send it to gmx-users-requ...@gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> >
> >
> >
> > --
> > With Best Wishes
> > Venkat Reddy Chirasani
> > PhD student
> > Laboratory of Computational Biophysics
> > Department of Biotechnology
> > IIT Madras
> > Chennai
> > INDIA-600036
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
> gmx-users mailing listgmx-users@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] 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



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

Sent from the GROMACS Users Forum mailing list archive at Nabble.com.







--
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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[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: 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 
> To: Discussion list for GROMACS users 
> 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
> wrote:
>
> > 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
> --
> 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
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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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



--
View this message in context: 
http://gromacs.5086.n6.nabble.com/Lipids-and-virtual-site-in-4-6-1-tp5007063.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.




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