date:20101226

RE: [gmx-users] Replicating an experiment

2010-12-26 Thread NG HUI WEN

Thanks Mark, message noted:)

-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham
Sent: Sunday, December 26, 2010 6:03 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Replicating an experiment

On 26/12/2010 4:37 AM, NG HUI WEN wrote:
> Thank you David for your prompt and useful reply :)  I am in fact
simulating a membrane protein.
>
> It's good to know I can use the "generate-new-starting-velocity"
method. But, do you mind to elaborate a bit more what you mean by "if
you simulate long enough"?
>
> I would like to try your suggestion of picking a random structure from
an elevated temperature simulation. Can I achieve that by taking my
existing membrane protein system,
> 1) pass it through grompp with a new mdp (with higher temperature) to
produce a new .tpr file

Do be aware that density will change if you do NPT at different T, and 
you'll need to re-equilibrate regardless.

Mark

> 2) simulate the system for a period (perhaps 1 ns)
> 3) take any frame / final structure
> 4) pass it through grompp again (with original mdp with temperature
300K, gen_seed = -1) to produce the .tpr file for my replicate?
>
> Thanks very much indeed!!
>
> 
>
> From: gmx-users-boun...@gromacs.org on behalf of David van der Spoel
> Sent: Sat 12/25/2010 10:28 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Replicating an experiment
>
>
>
> On 2010-12-25 15.05, NG HUI WEN wrote:
>> Dear all,
>> Merry Xmas! I have a very quick question here which i'd like to pick
>> your brain on, would really appreciate a reply.
>> I am planning to replicate an experiment that I have carried out.
Just
>> wondering what is the best way to do it? I am thinking of changing
the
>> starting velocity of my system by setting a random number e.g
23412445
>> etc in the gen_seed section as below, not sure if it is meaningful to
do so?
>> gen_vel = yes
>> gen_temp = 300.0
>> gen_seed = random number
>> Thank you for your input!
> That will work fine, if you simulate long enough. Consider that the
> starting structure may also influence how different your results  will
> be, e.g. for a protein in water. For liquids there is no such problem.
> You can do a simulation and slightly elevated temperature and pick
> structures from that with a different random seed, in order to
randomize
> your simulations even more.
>> HW
>> <<
>>
>> This message and any attachment are intended solely for the addressee
>> and may contain confidential information. If you have received this
>> message in error, please send it back to me, and immediately delete
it.
>> Please do not use, copy or disclose the information contained in this
>> message or in any attachment. Any views or opinions expressed by the
>> author of this email do not necessarily reflect the views of the
>> University of Nottingham.
>>
>> This message has been checked for viruses but the contents of an
>> attachment may still contain software viruses which could damage your
>> computer system: you are advised to perform your own checks. Email
>> communications with the University of Nottingham may be monitored as
>> permitted by UK&  Malaysia legislation.
>>
>>   >>
>>
>
> --
> 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.se
http://folding.bmc.uu.se
> --
> 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
>
>
> <<  This message and any attachment are intended solely for the
addressee and may contain confidential information. If you have received
this message in error, please send it back to me, and immediately delete
it. Please do not use, copy or disclose the information contained in
this message or in any attachment. Any views or opinions expressed by
the author of this email do not necessarily reflect the views of the
University of Nottingham.
>
> This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage your
computer system: you are advised to perform your own checks. Email
communications with the University of Nottingham may be monitored as
permitted by UK&  Malaysia legislation.>>

-- 
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

Re: [gmx-users] umbrella sampling

2010-12-26 Thread Justin A. Lemkul




Poojari, Chetan wrote:

Hi,

I am working on membrane protein.

In umbrella sampling tutorial...we saw the pulling of the peptide A away 
from peptide B.

I want to pull the peptide deep into the hydrophobic core of the bilayer from 
outside (solvent environment).

Please can someone suggest me how to go about this.



The same principles as in the tutorial apply.  Choose a reference group 
(membrane), a pull group (peptide), and a pull direction.  You'll have to 
empirically adjust pull rate, force constant, etc to properly treat your system.


-Justin




Kind regards,
chetan.






Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://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

Re: [gmx-users] number of DD cells

2010-12-26 Thread Justin A. Lemkul




Poojari, Chetan wrote:

Hi Mark,

I ran on 48 processors.the error is:

The X-size of the box (5.312040) times the triclinic skew factor (1.00)
is smaller than the number of DD cells (6) times the smallest allowed cell
size (0.885281)



I would say this further confirms Mark's suspicions.  Whatever you're doing to 
the system is causing it to rapidly collapse, a behavior that is now independent 
of the number of DD cells.


-Justin



Kind regards, chetan


 From: gmx-users-boun...@gromacs.org
[gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham
[mark.abra...@anu.edu.au] Sent: 27 December 2010 00:25 To: Discussion list
for GROMACS users Subject: Re: [gmx-users] number of DD cells

On 27/12/2010 7:51 AM, Poojari, Chetan wrote:

Hi,

I am following umbrella sampling tutorial for my membrane protein system.

While running continuous pulling simulation (mdrun). under step five:
Generating Configurations of the tutorial. I get the below error.

The system ran initially but corrupted very soon with warning " The X-size
of the box (4.800448) times the triclinic skew factor (1.00) is smaller
than the number of DD cells (4) times the smallest allowed cell size
(1.20) "

I am using 64 cores with -npme = 16. I haven't set any -dds. My system box
size is  6 x 6 x 12 nm


That's a large box deformation... 6nm to 4.8nm. I'd say your system is 
probably blowing up, and that -dds 0.6 is hiding the symptoms. Try running on

fewer processors to see whether when the DD box size is larger whether you
get other explosion symptoms.

Mark -- 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


 

 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich 
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher 
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft

(stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M.
Schmidt 

 




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://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

RE: [gmx-users] number of DD cells

2010-12-26 Thread Poojari, Chetan

Hi Mark,

I ran on 48 processors.the error is:

The X-size of the box (5.312040) times the triclinic skew factor (1.00) is 
smaller than the number of DD cells (6) times the smallest allowed cell size 
(0.885281)


Kind regards,
chetan



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Mark Abraham [mark.abra...@anu.edu.au]
Sent: 27 December 2010 00:25
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] number of DD cells

On 27/12/2010 7:51 AM, Poojari, Chetan wrote:
> Hi,
>
> I am following umbrella sampling tutorial for my membrane protein system.
>
> While running continuous pulling simulation (mdrun). under step five: 
> Generating Configurations of the tutorial. I get the below error.
>
> The system ran initially but corrupted very soon with warning " The X-size of 
> the box (4.800448) times the triclinic skew factor (1.00) is smaller than 
> the number of DD cells (4) times the smallest allowed cell size (1.20) "
>
> I am using 64 cores with -npme = 16. I haven't set any -dds.
> My system box size is  6 x 6 x 12 nm

That's a large box deformation... 6nm to 4.8nm. I'd say your system is
probably blowing up, and that -dds 0.6 is hiding the symptoms. Try
running on fewer processors to see whether when the DD box size is
larger whether you get other explosion symptoms.

Mark
--
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



Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt


--
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

Re: [gmx-users] topolbuild1_3 install problem

2010-12-26 Thread Mark Abraham


On 26/12/2010 10:07 PM, gromacs564 wrote:

Hi all

I downloaded topolbuild1_3 from the GROMACS website,

and I run the command as follows:



"path: home/buct/topolbuild1_3 ??

# tar -xvf topolbuild1_3.tgz

#make -f Makefile ; (intel CPU) there were no any error messages.

then I write "export PATH=$PATH:/home/buct/topolbuild1_3 " into 
etc/profile(root)




Don't mess with root files unless it's essential. You have your own 
.profile file for a reason.



```

But When I type "topolbuild -h" I get "command not found",and I don't 
know how to deal it.




The path of the *current* shell has to be right. Editing the files that 
set the path for *new* shells doesn't do anything to the current shell.



can anyone tell me to install the topolbuild1_3 correctly?



Does it provide documentation, and have you read it?

Mark
--
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

Re: [gmx-users] number of DD cells

2010-12-26 Thread Mark Abraham


On 27/12/2010 7:51 AM, Poojari, Chetan wrote:

Hi,

I am following umbrella sampling tutorial for my membrane protein system.

While running continuous pulling simulation (mdrun). under step five: 
Generating Configurations of the tutorial. I get the below error.

The system ran initially but corrupted very soon with warning " The X-size of the 
box (4.800448) times the triclinic skew factor (1.00) is smaller than the number of 
DD cells (4) times the smallest allowed cell size (1.20) "

I am using 64 cores with -npme = 16. I haven't set any -dds.
My system box size is  6 x 6 x 12 nm


That's a large box deformation... 6nm to 4.8nm. I'd say your system is 
probably blowing up, and that -dds 0.6 is hiding the symptoms. Try 
running on fewer processors to see whether when the DD box size is 
larger whether you get other explosion symptoms.


Mark
--
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

Re: [gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group

2010-12-26 Thread Mark Abraham

On 27/12/2010 9:22 AM, WU Yanbin wrote:

Hi, Mark,

Thanks for the reply.

As suggested, I tried a "water in vacuum" case. Initially the water 
droplet is a cubic 4nm-by-4nm-by-4nm water box, located in the middle 
of the simulation box. Everywhere else is just vacuum. The simulation 
box size is 8nm by 8nm by 8nm. SPC/E model is used to describe 
interaction between water molecules.

Such system is first equilibrated with "steep" option.

The "mdrun" simulation goes with no problem with parallel running on 
32 cpus, even though there are occasionaly one or two water molecules 
move very fast (Mean square displacement being 200 times fast than 
bulk water) in the vacuum.

OK, that sounds like behaviour that might be expected... some molecules 
evaporate. Check the trajectory to be confident this is the situation.

When I switch to 64 cpus, the error "X particles communicated to PME 
node Y are more than a cell length out of the domain decomposition 
cell of their charge group" appears.

The most plausible reason for this is that the above evaporated 
molecules are moving so fast that they're doing what the error message 
says - travelling more than width of a box in one integration step. The 
DD implementation is predicated on that being impossible.

You might succeed by arranging for the largest possible internal DD cell 
diameter, i.e. a 4x4x4 DD. mdrun -npme 0 might choose this, otherwise 
use the hidden options to mdrun (use mdrun -hidden) to use that DD with 
-npme 0.

Otherwise, you'll need to accept the fact that there are "engineering" 
constraints on efficient parallelization algorithms, and not every 
situation can be catered for. For example, a simulation of a bulk LJ 
fluid would fail if you used so many processors that the cell diameter 
was too small with respect to the distribution of particle speeds.

Mark

Below is the parameter file I'm using.

integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 500

comm-mode= Linear
nstcomm  = 1
comm-grps=

energygrps   =

nstlist  = 1
ns_type  = grid
pbc  = xyz
rlist= 1.5

coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.5
epsilon-r= 1

vdw-type = Cut-off ;Switch
rvdw-switch  = 1.0
rvdw = 1.5

fourierspacing   = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

Tcoupl   = nose-hoover
tc-grps  = System
tau_t= 1.0
ref_t= 300

Pcoupl   = no ;Parrinello-Rahman ;no ;berendsen
Pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

gen_vel  = no
gen_temp = 300
gen_seed = 2008

constraints  = none
constraint-algorithm = Lincs
Shake-SOR= no
shake-tol= 1e-04
lincs-order  = 4
lincs-warnangle  = 30

energygrp_excl   =

Is there any parameters configuration wrong with the simulation? Or is 
there any way to go around this error?

Any tip is appreciated.
Thank you.

Best,
Yanbin

--

Message: 1
Date: Thu, 02 Dec 2010 17:24:18 +1100
From: Mark Abraham mailto:mark.abra...@anu.edu.au>>
Subject: Re: [gmx-users] How to suppress the error "X particles
   communicatedto PME node Y are more than a cell length
out of the
   domain  decomposition cell of their charge group"
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID: <4cf73b92.40...@anu.edu.au
>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 2/12/2010 4:16 PM, WU Yanbin wrote:
> Dear GMXers,
>
> I'm running a simulation of water contact angle measurement on
top of
> graphite surface.
> Initially a water cubic box is placed on two-layer graphite surface
> with the rest of the box being vacuum. The water droplet is relaxed
> during the simulation to develop a spherical shape.
>
> An error of "X particles communicated to PME node Y are more than a
> cell length out of the domain decomposition cell of their charge
> group" was encountered.
> And I have read the suggested solutions at the link below
>

http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_

[gmx-users] umbrella sampling

2010-12-26 Thread Poojari, Chetan

Hi,

I am working on membrane protein.

In umbrella sampling tutorial...we saw the pulling of the peptide A away 
from peptide B.

I want to pull the peptide deep into the hydrophobic core of the bilayer from 
outside (solvent environment).

Please can someone suggest me how to go about this.



Kind regards,
chetan.






Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt


--
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

[gmx-users] number of DD cells

2010-12-26 Thread Poojari, Chetan

Hi,

To my earlier post on number of DD cells.i included -dds 0.6 and everything 
seems to run fine.

Is this the possible solution to the error or is there other way to handle this 
warning ?


Kind regards,
chetan.





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt


--
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

Re: [gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group

2010-12-26 Thread WU Yanbin

Hi, Mark,

Thanks for the reply.

As suggested, I tried a "water in vacuum" case. Initially the water droplet
is a cubic 4nm-by-4nm-by-4nm water box, located in the middle of the
simulation box. Everywhere else is just vacuum. The simulation box size is
8nm by 8nm by 8nm. SPC/E model is used to describe interaction between water
molecules.

Such system is first equilibrated with "steep" option.

The "mdrun" simulation goes with no problem with parallel running on 32
cpus, even though there are occasionaly one or two water molecules move very
fast (Mean square displacement being 200 times fast than bulk water) in the
vacuum.

When I switch to 64 cpus, the error "X particles communicated to PME node Y
are more than a cell length out of the domain decomposition cell of their
charge group" appears.

Below is the parameter file I'm using.


integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 500

comm-mode= Linear
nstcomm  = 1
comm-grps=

energygrps   =

nstlist  = 1
ns_type  = grid
pbc  = xyz
rlist= 1.5

coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.5
epsilon-r= 1

vdw-type = Cut-off ;Switch
rvdw-switch  = 1.0
rvdw = 1.5

fourierspacing   = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

Tcoupl   = nose-hoover
tc-grps  = System
tau_t= 1.0
ref_t= 300

Pcoupl   = no ;Parrinello-Rahman ;no ;berendsen
Pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

gen_vel  = no
gen_temp = 300
gen_seed = 2008

constraints  = none
constraint-algorithm = Lincs
Shake-SOR= no
shake-tol= 1e-04
lincs-order  = 4
lincs-warnangle  = 30

energygrp_excl   =


Is there any parameters configuration wrong with the simulation? Or is there
any way to go around this error?

Any tip is appreciated.
Thank you.

Best,
Yanbin




>
> --
>
> Message: 1
> Date: Thu, 02 Dec 2010 17:24:18 +1100
> From: Mark Abraham 
> Subject: Re: [gmx-users] How to suppress the error "X particles
>communicatedto PME node Y are more than a cell length out of the
>domain  decomposition cell of their charge group"
> To: Discussion list for GROMACS users 
> Message-ID: <4cf73b92.40...@anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 2/12/2010 4:16 PM, WU Yanbin wrote:
> > Dear GMXers,
> >
> > I'm running a simulation of water contact angle measurement on top of
> > graphite surface.
> > Initially a water cubic box is placed on two-layer graphite surface
> > with the rest of the box being vacuum. The water droplet is relaxed
> > during the simulation to develop a spherical shape.
> >
> > An error of "X particles communicated to PME node Y are more than a
> > cell length out of the domain decomposition cell of their charge
> > group" was encountered.
> > And I have read the suggested solutions at the link below
> >
> http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group
> .
> >
> > I guess the reason for this error in my case is because of the vacuum
> > such that the water molecules at the boundary of the droplet can move
> > fast. I have check the trajectory and the simulation is OK.
>
> I doubt the simulation is OK. This error message is one of several that
> can happen when the system is not well-enough conditioned for the MD to
> be stable. See www.gromacs.org/Documentation/Terminology/Blowing_Up.
> Here, you have atoms moving much faster than GROMACS was engineered to
> expect.
>
> You should be confident that a water drop in a vacuum, and your graphite
> surface are both stable on their own before you try the wetting simulation.
>
> >
> > For this situation, is there a way of suppressing this error? Or what
> > else can I do?
>
> Work out why it's poorly conditioned.
>
> Mark
>
-- 
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-us

[gmx-users] number of DD cells

2010-12-26 Thread Poojari, Chetan

Hi,

I am following umbrella sampling tutorial for my membrane protein system.

While running continuous pulling simulation (mdrun). under step five: 
Generating Configurations of the tutorial. I get the below error.

The system ran initially but corrupted very soon with warning " The X-size of 
the box (4.800448) times the triclinic skew factor (1.00) is smaller than 
the number of DD cells (4) times the smallest allowed cell size (1.20) "

I am using 64 cores with -npme = 16. I haven't set any -dds.
My system box size is  6 x 6 x 12 nm



Please can I know what might be the problem.


Kind regards,
chetan.



Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt


--
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

[gmx-users] Re: average pressure too high

2010-12-26 Thread Vitaly Chaban

>
> On Sun, Dec 26, 2010 at 12:28 AM, sreelakshmi ramesh <
> sree.laks...@research.iiit.ac.in> wrote:
>
>> Dear users,
>>                  I did nvt equil and after that npt equilbriation and i am
>> using parinello rahman as the barostat but the prob is even after 200 ps of
>> equil the avg pressure is 1.5 bar .can anybody hepl me out with the
>> issue.Any suggestions please.
>>
>> sree.


I believe pressure is something that one should not perceive very
seriously if he/she wants to succeed with MD simulations...  :-)



Dr. Vitaly V. Chaban               |  skype: vvchaban
Department of Chemistry       |  email: v.cha...@rochester.edu
University of Rochester          |  email: vvcha...@gmail.com
Rochester, NY 14627-0216    |  email: cha...@univer.kharkov.ua
United States of America        |  chem.rochester.edu/~prezhdo_group
--
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

Re: [gmx-users] amb2gmx.pl file

2010-12-26 Thread Oliver Grant

Hi Xiaodu,

The fudgeLJ under defaults should be 1.0 for GLYCAM. I'm unable to check my
own files right now so can't compare. When you run grompp check in the
output that fudge is set to 1.0. So there will be no protein in your
simulation correct? I think there is a way to do mixed scaling in gromacs
but I haven't looked into it.

Oliver

2010/12/25 gromacs564 

> Hi  Alan , Oliver
>  I have obtained the gromacs format files by amb2gmx.pl script, but I
> am not sure if this flies are correct ,
> because all of the [pairs](1-4 interaction) are zero in gromacs top files.
> I don't know whether this files are correct or not.
>  Would you give me some advice? Thank your very much.
>
> all the best
> xiaodu
>
> 
>
> -
> ; lambda.top created by rdparm2gmx.pl Fri Dec 24 10:22:31 CST 2010
> [ defaults ]
> ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
> 1   2   yes 0.5 0.8333
> [ atomtypes ]
> ;name  bond_typemasscharge   ptype  sigma  epsilon
> HOHO  0.  0.  A   0.0e+00  0.0e+00
> H1H1  0.  0.  A   2.47135e-01  6.56888e-02
> OSOS  0.  0.  A   3.1e-01  7.11280e-01
> CGCG  0.  0.  A   3.39967e-01  4.57730e-01
> H2H2  0.  0.  A   2.29317e-01  6.56888e-02
> OHOH  0.  0.  A   3.06647e-01  8.80314e-01
> [ moleculetype ]
> ; Namenrexcl
> solute 3
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr charge   mass
> typeBchargeB
>  1 HO  1ROHHO1  10.44500   1.00
>  2 OH  1ROH O1  2   -0.63900  16.00
>  3 CG  24GA C1  30.50900  12.00
>  4 H2  24GA H1  40.0   1.00
>  5 CG  24GA C2  50.24600  12.00
>  6 H1  24GA H2  60.0   1.00
>  7 OH  24GA O2  7   -0.71300  16.00
>  8 HO  24GAH2O  80.43700   1.00
>  9 CG  24GA C3  90.28600  12.00
> 10 H1  24GA H3 100.0   1.00
> 11 OH  24GA O3 11   -0.69900  16.00
> 12 HO  24GAH3O 120.42700   1.00
> 13 CG  24GA C4 130.25400  12.00
> 14 H1  24GA H4 140.0   1.00
> 15 CG  24GA C5 150.28300  12.00
> 16 H1  24GA H5 160.0   1.00
> 17 OS  24GA O5 17   -0.57400  16.00
> 18 CG  24GA C6 180.27600  12.00
> 19 H1  24GAH61 190.0   1.00
> 20 H1  24GAH62 200.0   1.00
> 21 OH  24GA O6 21   -0.68200  16.00
> 22 HO  24GAH6O 220.41800   1.00
> 23 OS  24GA O4 23   -0.46800  16.00
> 24 CG  30GA C1 240.50900  12.00
> 25 H2  30GA H1 250.0   1.00
> 26 CG  30GA C2 260.24600  12.00
> 27 H1  30GA H2 270.0   1.00
> 28 OH  30GA O2 28   -0.71300  16.00
> 29 HO  30GAH2O 290.43700   1.00
> 30 CG  30GA C3 300.28600  12.00
> 31 H1  30GA H3 310.0   1.00
> 32 OH  30GA O3 32   -0.69900  16.00
> 33 HO  30GAH3O 330.42700   1.00
> 34 CG  30GA C4 340.25400  12.00
> 35 H1  30GA H4 350.0   1.00
> 36 OH  30GA O4 36   -0.71000  16.00
> 37 HO  30GAH4O 370.43600   1.00
> 38 CG  30GA C5 380.28300  12.00
> 39 H1  30GA H5 390.0   1.00
> 40 OS  30GA O5 40   -0.57400  16.00
> 41 CG  30GA C6 410.27600  12.00
> 42 H1  30GAH61 420.0   1.00
> 43 H1  30GAH62 430.0   1.00
> 44 OH  30GA O6 44   -0.68200  16.00
> 45 HO  30GAH6O 450.41800   1.00
> [ bonds ]
> ;  aiaj funct  r  k

Re: [gmx-users] average pressure too high

2010-12-26 Thread Roland Schulz

Hi,

what is the standard deviation and drift? Are you sure this is a significant
difference to 1?

Roland

On Sun, Dec 26, 2010 at 12:28 AM, sreelakshmi ramesh <
sree.laks...@research.iiit.ac.in> wrote:

> Dear users,
>  I did nvt equil and after that npt equilbriation and i am
> using parinello rahman as the barostat but the prob is even after 200 ps of
> equil the avg pressure is 1.5 bar .can anybody hepl me out with the
> issue.Any suggestions please.
>
> sree.
>
> --
> 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
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
-- 
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

[gmx-users] topolbuild1_3 install problem

2010-12-26 Thread gromacs564

 Hi all

I downloaded topolbuild1_3 from the GROMACS website,

and I run the command as follows:



"path: home/buct/topolbuild1_3 ”

# tar -xvf topolbuild1_3.tgz

#make -f Makefile ;   (intel CPU) there were no any  error messages.

then I write "export PATH=$PATH:/home/buct/topolbuild1_3 "  into 
etc/profile(root)

```

But When I type "topolbuild -h" I get "command not found",and I don't know how 
to deal it.

can anyone tell me to install the topolbuild1_3 correctly?

 Thank you!

xiaodu


 

 



-- 
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

[gmx-users] topolbuild1_3 install problem

2010-12-26 Thread gromacs564

Hi all

I downloaded topolbuild1_3 from the GROMACS website,

and I run the command as follows:



"path: home/buct/topolbuild1_3 ”

# tar -xvf topolbuild1_3.tgz

#make -f Makefile ;   (intel CPU) there were no any  error messages.

then I write "export PATH=$PATH:/home/buct/topolbuild1_3 "  into 
etc/profile(root)

```

But When I type "topolbuild -h" I get "command not found",and I don't know how 
to deal it.

can anyone tell me to install the topolbuild1_3 correctly?

 Thank you!


 

 -- 
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

Re: [gmx-users] Replicating an experiment

2010-12-26 Thread Mark Abraham


On 26/12/2010 4:37 AM, NG HUI WEN wrote:

Thank you David for your prompt and useful reply :)  I am in fact simulating a 
membrane protein.

It's good to know I can use the "generate-new-starting-velocity" method. But, do you mind 
to elaborate a bit more what you mean by "if you simulate long enough"?

I would like to try your suggestion of picking a random structure from an 
elevated temperature simulation. Can I achieve that by taking my existing 
membrane protein system,
1) pass it through grompp with a new mdp (with higher temperature) to produce a 
new .tpr file


Do be aware that density will change if you do NPT at different T, and 
you'll need to re-equilibrate regardless.


Mark


2) simulate the system for a period (perhaps 1 ns)
3) take any frame / final structure
4) pass it through grompp again (with original mdp with temperature 300K, 
gen_seed = -1) to produce the .tpr file for my replicate?

Thanks very much indeed!!



From: gmx-users-boun...@gromacs.org on behalf of David van der Spoel
Sent: Sat 12/25/2010 10:28 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Replicating an experiment



On 2010-12-25 15.05, NG HUI WEN wrote:

Dear all,
Merry Xmas! I have a very quick question here which i'd like to pick
your brain on, would really appreciate a reply.
I am planning to replicate an experiment that I have carried out. Just
wondering what is the best way to do it? I am thinking of changing the
starting velocity of my system by setting a random number e.g 23412445
etc in the gen_seed section as below, not sure if it is meaningful to do so?
gen_vel = yes
gen_temp = 300.0
gen_seed = random number
Thank you for your input!

That will work fine, if you simulate long enough. Consider that the
starting structure may also influence how different your results  will
be, e.g. for a protein in water. For liquids there is no such problem.
You can do a simulation and slightly elevated temperature and pick
structures from that with a different random seed, in order to randomize
your simulations even more.

HW
<<

This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
message in error, please send it back to me, and immediately delete it.
Please do not use, copy or disclose the information contained in this
message or in any attachment. Any views or opinions expressed by the
author of this email do not necessarily reflect the views of the
University of Nottingham.

This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage your
computer system: you are advised to perform your own checks. Email
communications with the University of Nottingham may be monitored as
permitted by UK&  Malaysia legislation.

  >>



--
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
--
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


<<  This message and any attachment are intended solely for the addressee and 
may contain confidential information. If you have received this message in error, 
please send it back to me, and immediately delete it. Please do not use, copy or 
disclose the information contained in this message or in any attachment. Any views or 
opinions expressed by the author of this email do not necessarily reflect the views 
of the University of Nottingham.

This message has been checked for viruses but the contents of an attachment may still 
contain software viruses which could damage your computer system: you are advised to 
perform your own checks. Email communications with the University of Nottingham may be 
monitored as permitted by UK&  Malaysia legislation.>>


--
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

Re: [gmx-users] No such moleculetype NA+

2010-12-26 Thread YUVRAJ UBOVEJA

Hello Shikha

Replace NA+ with NA in your topol.top file.
It will solve the problem as it recognise NA for NA+.

Thanks

Yuvraj
IIIT Hyderabad

On Sun, Dec 26, 2010 at 12:26 PM,  wrote:

> Send gmx-users mailing list submissions to
>gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
>gmx-users-requ...@gromacs.org
>
> You can reach the person managing the list at
>gmx-users-ow...@gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
> Today's Topics:
>
>   1. Re: Replicating an experiment (David van der Spoel)
>   2. RE: Replicating an experiment (NG HUI WEN)
>   3. average pressure too high (sreelakshmi ramesh)
>   4. No such moleculetype NA+ (shikha agarwal)
>
>
> -- Forwarded message --
> From: David van der Spoel 
> To: Discussion list for GROMACS users 
> Date: Sat, 25 Dec 2010 22:55:34 +0100
> Subject: Re: [gmx-users] Replicating an experiment
> On 12/25/10 6:37 PM, NG HUI WEN wrote:
>
>> Thank you David for your prompt and useful reply :)  I am in fact
>> simulating a membrane protein.
>>
>> It's good to know I can use the "generate-new-starting-velocity" method.
>> But, do you mind to elaborate a bit more what you mean by "if you simulate
>> long enough"?
>>
>> I would like to try your suggestion of picking a random structure from an
>> elevated temperature simulation. Can I achieve that by taking my existing
>> membrane protein system,
>> 1) pass it through grompp with a new mdp (with higher temperature) to
>> produce a new .tpr file
>> 2) simulate the system for a period (perhaps 1 ns)
>> 3) take any frame / final structure
>> 4) pass it through grompp again (with original mdp with temperature 300K,
>> gen_seed = -1) to produce the .tpr file for my replicate?
>>
>>  Yes that is what I meant. Of course you should check that your protein is
> not unfolding, or you membrane going into the wrong phase.
>
>  Thanks very much indeed!!
>>
>> 
>>
>> From: gmx-users-boun...@gromacs.org on behalf of David van der Spoel
>> Sent: Sat 12/25/2010 10:28 PM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] Replicating an experiment
>>
>>
>>
>> On 2010-12-25 15.05, NG HUI WEN wrote:
>>
>>> Dear all,
>>> Merry Xmas! I have a very quick question here which i'd like to pick
>>> your brain on, would really appreciate a reply.
>>> I am planning to replicate an experiment that I have carried out. Just
>>> wondering what is the best way to do it? I am thinking of changing the
>>> starting velocity of my system by setting a random number e.g 23412445
>>> etc in the gen_seed section as below, not sure if it is meaningful to do
>>> so?
>>> gen_vel = yes
>>> gen_temp = 300.0
>>> gen_seed = random number
>>> Thank you for your input!
>>>
>> That will work fine, if you simulate long enough. Consider that the
>> starting structure may also influence how different your results  will
>> be, e.g. for a protein in water. For liquids there is no such problem.
>> You can do a simulation and slightly elevated temperature and pick
>> structures from that with a different random seed, in order to randomize
>> your simulations even more.
>>
>>> HW
>>> <<
>>>
>>> This message and any attachment are intended solely for the addressee
>>> and may contain confidential information. If you have received this
>>> message in error, please send it back to me, and immediately delete it.
>>> Please do not use, copy or disclose the information contained in this
>>> message or in any attachment. Any views or opinions expressed by the
>>> author of this email do not necessarily reflect the views of the
>>> University of Nottingham.
>>>
>>> This message has been checked for viruses but the contents of an
>>> attachment may still contain software viruses which could damage your
>>> computer system: you are advised to perform your own checks. Email
>>> communications with the University of Nottingham may be monitored as
>>> permitted by UK&  Malaysia legislation.
>>>
>>>  >>
>>>
>>>
>>
>> --
>> 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<
>> http://folding.bmc.uu.se/>
>> --
>> 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
>>
>>
>> <<  This message and any attachment are intended solely for the addressee
>> and may contain confi

RE: [gmx-users] Replicating an experiment

Re: [gmx-users] umbrella sampling

Re: [gmx-users] number of DD cells

RE: [gmx-users] number of DD cells

Re: [gmx-users] topolbuild1_3 install problem

Re: [gmx-users] number of DD cells

Re: [gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group

[gmx-users] umbrella sampling

[gmx-users] number of DD cells

Re: [gmx-users] How to suppress the error "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group

[gmx-users] number of DD cells

[gmx-users] Re: average pressure too high

Re: [gmx-users] amb2gmx.pl file

Re: [gmx-users] average pressure too high

[gmx-users] topolbuild1_3 install problem

[gmx-users] topolbuild1_3 install problem

Re: [gmx-users] Replicating an experiment

Re: [gmx-users] No such moleculetype NA+

18 matches

Site Navigation

Mail list logo

Footer information