[gmx-users] Is GPU GTX 560 compatible with GROMACS?

[Gaurav Goel]

Dear All,

Can you please guide me on how to find out if GeForce GTX 560 GPU card
by NVIDIA will be compatible with GROMACS? On the website GTX 560 Ti
is mentioned, but GTX 560 is not.

Thanks,
G

-- 
Gaurav Goel, PhD
Assistant Professor
Department of Chemical Engineering
Indian Institute of Technology, Delhi
Hauz Khas, New Delhi 110016
India
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[gmx-users] Pseudo 2-D Ewald Summation and Slab Geometry

[Andrew DeYoung]

Hi, 

I am simulating a capacitor (in which the dielectric is liquid between the
plates), with charged electrodes parallel to the xy plane.  Because the
system is effectively two-dimensional, I am using ewald_geometry = 3dc,
which applies a force and potential correction in the z dimension, giving a
pseudo 2-D Ewald summation.  

However, I observe a drift in the electric potential between the plates.
Specifically, I use g_potential to solve the Poisson equation and determine
the electric potential as a function of the z coordinate.  The liquid has a
structure such that an electric double layer is formed, and this cancels off
much of the electric field due to the charged electrodes.  So, I would
expect that the potential between the plates is constant (i.e., a plot of
the electric potential Phi versus z is expected to be flat).  This is in
fact what I observe when I simulate the same system using another MD
package, using exactly the same force field parameters and the analogous
(same correction equations, just different code) force and potential
correction in the z dimension to produce a pseudo 2-D Ewald summation: in
that other MD package, the electric potential is constant (flat) between the
capacitor plates.  But in Gromacs (4.5.5), the potential is not constant
(flat) between the plates; rather, it is linear with a non-zero slope.

Has anyone else experienced such a "drift" in the electric potential when
using a slab geometry and ewald_geometry = 3dc?  Do you have any ideas of
what might cause this and how I can fix this?  

Thank you very much.

Andrew DeYoung
Carnegie Mellon University

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Re: [gmx-users] File editing - only one layer of water around a molecule

[Teemu Murtola]

On Fri, Apr 13, 2012 at 18:30, Lara Bunte  wrote:
> Is there no way only to use the .pdb file? How do I create from a .pdb a rtp
> file. With pdb2gmx and than grompp?

You can also provide a .pdb file to the -s option of g_select. And you
don't need to provide a -f file in that case if you simply want to
analyze the coordinates in a single configuration of that .pdb file.

Best regards,
Teemu
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Re: [gmx-users] File editing - only one layer of water around a molecule

[Justin A. Lemkul]

Lara Bunte wrote:

Hi

You are totally right. I am sorry. It is just so frustrating if you read 
the complete help more than once, understand nothing and than here all 
the time, that I should read the help. :-(


I like Gromacs and I am happy that it is free and I am very thankful for 
all the help here in the mailing list.


But I also have to say (please don't take this an attack): If you are a 
total beginner and have no good knowledge about basic chemistry, it is 
really tough and frustrating reading the manual and help. There should 
be more help, especially how to type it in. Not everywhere but in the 
i.e. in the beginning of the manual a few words about that. 

I am from engineering and now I am in the physical chemistry. I want to 
learn! I am reading in the manual, the tutorials and in Chemistry for 
beginner books, but all the stuff is pretty hard if you are new in the 
topic




If you're new to chemistry, and especially computational chemistry, then you're 
not only trying to learn chemistry, but Linux/Unix and specialized software that 
makes use of it.  That is usually too much at once and leads to frustration. 
You have to learn to walk before you can run.  When we train new members of our 
lab, it's a stepwise process and they usually spend a few weeks or months 
learning basic (and unfortunately, sometimes repetitive and boring) things 
before we even let them touch anything useful or truly productive ;)  Certain 
prerequisites are assumed, and by necessity, have to be, otherwise the Gromacs 
manual becomes bloated by recapitulating information that is already well 
covered in other places.



About the topic:

Is there no way only to use the .pdb file? How do I create from a .pdb a 
rtp file. With pdb2gmx and than grompp?




Please note that I said .tpr file, not .rtp.  They are wildly different.  The 
.tpr file is used to run a simulation, which I suspect we all assumed was 
something you had done and thus had accessible to you.  A coordinate file and 
corresponding topology, coupled with an .mdp file, are needed to assemble the 
.tpr file using grompp.


-Justin

--


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


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Re: [gmx-users] progressive imbalance in REMD

[Mark Abraham]

On 14/04/2012 1:46 AM, francesco oteri wrote:

Dear gromacs users,
I am running REMD through gromacs 4.5.5 using 10replicas.
I am experiencing a problem with simulation efficiency, in particular 
from gromacs output, like the following:
vol 0.49  imb F  4% vol 0.64  imb F  8% vol 0.17  imb F  2% vol 0.56 
 imb F 10% vol 0.17! imb F  7% vol 0.75  imb F 11% vol 0.45  imb F 11% 
vol 0.13! imb F  8% vol 0.45  imb F 16% vol 0.55  imb F 23% step 
735900, will finish Mon Apr 16 07:29:53 2012


it seems that higher temperature replicas suffer of an higher 
imbalance between force and PME.



These are the average values:

4.58991117815
5.5175129881
6.32679738562
7.21887045416
8.1979219038
9.45466733702
10.9115133233
12.5899111781
15.0987095693
19.5630970337

Of course this problem impacts on overall performances.

My questions are:
1) Is the progressive imbalance expected?
2) Is there any way to alleviate the problem?


Guessing wildly in the absence of a description, you're running NPT 
REMD, and so the particle density changes with T, so the nonbonded cost 
varies with T while the PME cost does not. The timing breakdown at the 
end of the individual .log files may prove informative in this respect. 
This problem snowballs - your generalized ensemble can only progress at 
the rate of your slowest contributing ensemble. In theory, one could 
develop a scheme where the PME performance and accuracy was 
near-constant with respect to T by varying the cutoff, splitting 
parameter and Fourier grid, but since most people choose their PME 
parameters by copying people who pulled near-arbitrary numbers out of 
the air, this would seem to be overkill.


People often do NVT REMD to avoid this effect if they are interested 
only in the ensemble at one temperature. That means the 
higher-temperature replicas have unphysically high pressures, which 
might or might not prove to be useful for enhanced sampling. Some people 
think that makes the sampling at the low temperature bogus, but I have 
never seen a convincing argument that all the replicas should correspond 
to a physical ensemble that closely resembles the target ensemble.


Mark
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Re: [gmx-users] progressive imbalance in REMD

[David van der Spoel]

On 2012-04-13 17:46, francesco oteri wrote:

Dear gromacs users,
I am running REMD through gromacs 4.5.5 using 10replicas.
I am experiencing a problem with simulation efficiency, in particular
from gromacs output, like the following:
vol 0.49  imb F  4% vol 0.64  imb F  8% vol 0.17  imb F  2% vol 0.56
  imb F 10% vol 0.17! imb F  7% vol 0.75  imb F 11% vol 0.45  imb F 11%
vol 0.13! imb F  8% vol 0.45  imb F 16% vol 0.55  imb F 23% step 735900,
will finish Mon Apr 16 07:29:53 2012

it seems that higher temperature replicas suffer of an higher imbalance
between force and PME.


These are the average values:

4.58991117815
5.5175129881
6.32679738562
7.21887045416
8.1979219038
9.45466733702
10.9115133233
12.5899111781
15.0987095693
19.5630970337

Of course this problem impacts on overall performances.

My questions are:
1) Is the progressive imbalance expected?

Yes, due to lower density.


2) Is there any way to alleviate the problem?

No.




Francesco





--
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] progressive imbalance in REMD

[francesco oteri]

Dear gromacs users,
I am running REMD through gromacs 4.5.5 using 10replicas.
I am experiencing a problem with simulation efficiency, in particular from
gromacs output, like the following:
vol 0.49  imb F  4% vol 0.64  imb F  8% vol 0.17  imb F  2% vol 0.56  imb F
10% vol 0.17! imb F  7% vol 0.75  imb F 11% vol 0.45  imb F 11% vol 0.13!
imb F  8% vol 0.45  imb F 16% vol 0.55  imb F 23% step 735900, will finish
Mon Apr 16 07:29:53 2012

it seems that higher temperature replicas suffer of an higher imbalance
between force and PME.


These are the average values:

4.58991117815
5.5175129881
6.32679738562
7.21887045416
8.1979219038
9.45466733702
10.9115133233
12.5899111781
15.0987095693
19.5630970337

Of course this problem impacts on overall performances.

My questions are:
1) Is the progressive imbalance expected?
2) Is there any way to alleviate the problem?


Francesco
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Re: [gmx-users] File editing - only one layer of water around a molecule

[Lara Bunte]

Hi

You are totally right. I am sorry. It is just so frustrating if you read the 
complete help more than once, understand nothing and than here all the time, 
that I should read the help. :-(

I like Gromacs and I am happy that it is free and I am very thankful for all 
the help here in the mailing list. 


But I also have to say (please don't take this an attack): If you are a total 
beginner and have no good knowledge about basic chemistry, it is really tough 
and frustrating reading the manual and help. There should be more help, 
especially how to type it in. Not everywhere but in the i.e. in the beginning 
of the manual a few words about that. 

I am from engineering and now I am in the physical chemistry. I want to learn! 
I am reading in the manual, the tutorials and in Chemistry for beginner books, 
but all the stuff is pretty hard if you are new in the topic


About the topic:

Is there no way only to use the .pdb file? How do I create from a .pdb a rtp 
file. With pdb2gmx and than grompp?

Greetings
Lara







 Von: Justin A. Lemkul 
An: Discussion list for GROMACS users  
Gesendet: 15:40 Freitag, 13.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a 
molecule
 


Lara Bunte wrote:
> Hi Justin
> 
> Okay, after
> 
> g_select -f mol_in_water.pdb -select '"Close to ISO" resname SOL and within 
> 0.5 of group "ISO"'
> 
> I got:
> 
> selection parser: invalid selection '"Close to ISO" resname SOL and within 
> 0.5 of group "ISO"'
> 
> Input error or input inconsistency:
> selection(s) could not be parsed
> 
> I also tried other permutations of ISO and SOL and got the same.
> 
> I read the complete help to g_select twice and I understand nothing what 
> there is written.  In general I like Gromacs more and more but g_select 
> program is totally fucked. I don't get it. :-(
> 

There is absolutely no need for crude language.  We all understand frustration, 
but insulting someone else's work, especially in this manner, is unprofessional 
and uncalled for.  The development of g_select required a heroic amount of 
effort.  It is a complicated program, to be sure, and the documentation is 
improving (as is true for all Gromacs programs, to differing extents).  How 
much did you pay for Gromacs?  How much do you pay for technical support?  Keep 
that in mind.  I'm not easily offended, but the other several thousand users of 
this list might become highly unlikely to help a hothead who could curse them 
out if the proper answer isn't received.

Provide a .tpr file to the -s flag of g_select; it should solve the problem.

> Greetings
> Lara
> 
> p.s.
> Here in this email if I got to answer (like always) is only Justins mail 
> adress, not the gromacs user list. I do it in cc
> 

Configure your mail client to reply-all by default or replace the address.

-Justin

> 
> 
> 
> 
> *Von:* Justin A. Lemkul 
> *An:* Lara Bunte ; Discussion list for GROMACS users 
> 
> *Gesendet:* 14:59 Freitag, 13.April 2012
> *Betreff:* Re: [gmx-users] File editing - only one layer of water around a 
> molecule
> 
> 
> 
> Lara Bunte wrote:
>  > Hi
>  >
>  > I tried but I got an error. In my mol_in_water.pdb file all atoms of my 
>molecule has the group notation ISO and all the water atoms has the group 
>notation SOL. I used following command:
>  >
>  > g_select -f my mol_in_water.pdb -other -options -select '"Close to ISO" 
>resname SOL and within 0.5 of group "ISO"'
>  >
>  > and I got the error:
>  >
>  > Invalid command line argument:
>  > -other
>  >
>  > How can I fix it.
>  >
> 
> Please see g_select -h for valid options.  Mark was simply implying that you 
> will likely need other command line options to make the program actually do 
> something.  Also note the space in your "my mol_in_water.pdb" will cause 
> problems as well.
> 
> -Justin
> 
> -- 
> 
> 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
> 
> 
> 
> 

-- 

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


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gmx-users mailing

Re: [gmx-users] File editing - only one layer of water around a molecule

[Justin A. Lemkul]

Lara Bunte wrote:

Hi Justin

Okay, after

g_select -f mol_in_water.pdb -select '"Close to ISO" resname SOL and 
within 0.5 of group "ISO"'


I got:

selection parser: invalid selection '"Close to ISO" resname SOL and 
within 0.5 of group "ISO"'


Input error or input inconsistency:
selection(s) could not be parsed

I also tried other permutations of ISO and SOL and got the same.

I read the complete help to g_select twice and I understand nothing what 
there is written.  In general I like Gromacs more and more but g_select 
program is totally fucked. I don't get it. :-(




There is absolutely no need for crude language.  We all understand frustration, 
but insulting someone else's work, especially in this manner, is unprofessional 
and uncalled for.  The development of g_select required a heroic amount of 
effort.  It is a complicated program, to be sure, and the documentation is 
improving (as is true for all Gromacs programs, to differing extents).  How much 
did you pay for Gromacs?  How much do you pay for technical support?  Keep that 
in mind.  I'm not easily offended, but the other several thousand users of this 
list might become highly unlikely to help a hothead who could curse them out if 
the proper answer isn't received.


Provide a .tpr file to the -s flag of g_select; it should solve the problem.


Greetings
Lara

p.s.
Here in this email if I got to answer (like always) is only Justins mail 
adress, not the gromacs user list. I do it in cc




Configure your mail client to reply-all by default or replace the address.

-Justin






*Von:* Justin A. Lemkul 
*An:* Lara Bunte ; Discussion list for GROMACS 
users 

*Gesendet:* 14:59 Freitag, 13.April 2012
*Betreff:* Re: [gmx-users] File editing - only one layer of water around 
a molecule




Lara Bunte wrote:
 > Hi
 >
 > I tried but I got an error. In my mol_in_water.pdb file all atoms of 
my molecule has the group notation ISO and all the water atoms has the 
group notation SOL. I used following command:

 >
 > g_select -f my mol_in_water.pdb -other -options -select '"Close to 
ISO" resname SOL and within 0.5 of group "ISO"'

 >
 > and I got the error:
 >
 > Invalid command line argument:
 > -other
 >
 > How can I fix it.
 >

Please see g_select -h for valid options.  Mark was simply implying that 
you will likely need other command line options to make the program 
actually do something.  Also note the space in your "my 
mol_in_water.pdb" will cause problems as well.


-Justin

-- 

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






--


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


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[gmx-users] Re: g_wham problem with negative COM differences

[Thomas Schlesier]

Anni Kauko wrote:
> >
> > Date: Wed, 11 Apr 2012 08:38:05 -0400
> > From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
> > Subject: Re: [gmx-users] g_wham problem with negative COM 
differences

> > To: Discussion list for GROMACS users  > >
> > Message-ID: <4f857b2d.3050...@vt.edu 
>

> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >
> >
> > Anni Kauko wrote:
> >  > Hi!
> >  >
> >  > I try to perform pmf calculations for case where a peptide 
shifts

> >  > through the membrane. My COM differences should vary from 2.3 to
> > -2.5.
> >  >
> >  > My problem is that g_wham plots negative COM difference as they
> > would be
> >  > positive.  In pullx-files the COM differences are treated 
correctly
> >  > (look below). My peptide is not symmetric, so profile curves 
are not
> >  > symmetric, so loosing the sign for COM difference screws my 
profile

> >  > curve completely.
> >  >
> >  > I did not manage to find any pre-existing answers to this 
problem

> > from
> >  > internet.
> >  >
> >  > First datalines from pullx files:
> >  > (sorry for strange file names...)
> >  >
> >  > pull_umbr_0.xvg:
> >  > 0.  6.26031 2.27369
> >  >
> >  > pullz_umbr_23.xvg:
> >  > 0.  6.09702 0.0233141
> >  >
> >  > pullz_umbr_50.xvg:
> >  > 0.  6.02097 -2.50088
> >  >
> >  > g_wham command:
> >  > g_wham -b 5000 -it tpr_files.dat  -ix pullz_files.dat -o
> >  > profile_test.xvg -hist histo_test.xvg  -unit kCal
> >  >
> >  > My pull code:
> >  >
> >  > pull= umbrella
> >  > pull_geometry   = distance
> >  > pull_dim= N N Y
> >  > pull_start  = yes
> >  > pull_ngroups= 1
> >  > pull_group0 = POPC_POPS ; reference group is bilayer
> >  > pull_group1 = C-alpha_&_r_92-94 ; group that is actually 
pulled

> >  > pull_init1  = 0
> >  > pull_rate1  = 0.0
> >  > pull_k1 = 1000 ; kJ mol-1 nm-2
> >  >
> >
> > Your problem stems from the use of "distance" geometry.  This 
method

> > assumes the
> > sign along the reaction coordinate does not change, i.e. always
> > positive or
> > always negative.  If the sign changes, this simple method fails.
> >  You should be
> > using something like "position" to allow for a vector to be
> > specified.  Perhaps
> > you can reconstruct the PMF by separately analyzing the positive
> > restraint
> > distances and negative restraint distances (note here that
> > "distance" really
> > refers to a vector quantity, and thus it can have a sign), or
> > otherwise create
> > new .tpr files using "position" geometry, though I don't know if
> > g_wham will
> > accept them or not.
> >
> > -Justin
> >
> > --
> > 
> >
> > 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
> >
> > 
> >
> >
> > Thank's!
> >
> > I managed to solve my g_wham problem by doing two things:
> >
> > 1. New tpr-files with proper pull code for g_wham.
> > 2. I also needed to modify signs of pullf values: If value for pullx
> > distance was negative, I reversed the sign of corresponding pullf 
value.

> > I did that by my own script.
> >
> > The new pull code:
> >
> > ; Pull code
> >
> > pull= umbrella
> > pull_geometry   = direction
> > pull_vec1   = 0 0 1
> > pull_start  = yes
> > pull_ngroups= 1
> > pull_group0 = POPC_POPS ; reference group is bilayer
> > pull_group1 = C-alpha_&_r_92-94 ; group that is actually pulled
> > pull_init1  = 0
> > pull_rate1  = 0.0
> > pull_k1 = 1000 ; kJ mol-1 nm-2
> >
> > I am little bit confuced, why I needed to tweak signes of pullf 
values.

> > But like that I got the curve that resembles two half curve made for
> > positive and negative pullx distances separately. That curve also 
makes

> > sense from biochemical point of view.
> >
>Such changes do not seem appropriate to me.  If you change the sign of 
>the
>pulling force, you change the implication of what that value means. 
>What
>happens if you run your simulations with the new (more appropriate) 
>.mdp file?

>Do the forces have the same magnitude, but opposite sign?

I don't think that the problem is so easy fixed. I had with another 
person about a month ago a lengthy discussion on the list.


The problem is the following:
If you use 'distance' as pull_geometry the position of the minimum of 
the 

Re: [gmx-users] a question related to production MD

[Justin A. Lemkul]

Please keep the discussion on the mailing list.

Acoot Brett wrote:

Dear Justin,
 
My question is a reaction can occur in 2 direction, i.e., forward 
direction and reverse reaction. As for before the start of production MD 
the system has fully equilibrated, thus during the whole production MD 
there will be no significant energy change. But then why the system 
should converge, or vibrate around the converge conformation, rather 
than vibrate around the production MD start conformation?
 


Equilibration is typically done with restraints on the solute.  Thus, the data 
collection stage is the first time that the solute is allowed to move freely. 
Further, equilibration is typically far shorter in terms of time than the actual 
data collection phase.  The timeframe required for the collection of useful data 
varies depending upon the question being asked, but you need to always be 
mindful of the different lengths of time that it takes for various physically 
relevant behaviors to take place.  The extent of change observed between the 
starting an converged structures depends entirely upon the inherent behavior of 
the molecule(s) being studied.


-Justin

--


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


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[gmx-users] g_wham problem with negative COM differences

[Thomas Schlesier]

New try, think last time message didn't reached the list :(

 Original-Nachricht 
Betreff: Re: g_wham problem with negative COM differences
Datum: Fri, 13 Apr 2012 14:55:15 +0200
Von: Thomas Schlesier 
An: 

Anni Kauko wrote:

>
> Date: Wed, 11 Apr 2012 08:38:05 -0400
> From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
> Subject: Re: [gmx-users] g_wham problem with negative COM

differences

> To: Discussion list for GROMACS users  >
> Message-ID: <4f857b2d.3050...@vt.edu

>

> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Anni Kauko wrote:
>  > Hi!
>  >
>  > I try to perform pmf calculations for case where a peptide

shifts

>  > through the membrane. My COM differences should vary from 2.3 to
> -2.5.
>  >
>  > My problem is that g_wham plots negative COM difference as they
> would be
>  > positive.  In pullx-files the COM differences are treated

correctly

>  > (look below). My peptide is not symmetric, so profile curves

are not

>  > symmetric, so loosing the sign for COM difference screws my

profile

>  > curve completely.
>  >
>  > I did not manage to find any pre-existing answers to this

problem

> from
>  > internet.
>  >
>  > First datalines from pullx files:
>  > (sorry for strange file names...)
>  >
>  > pull_umbr_0.xvg:
>  > 0.  6.26031 2.27369
>  >
>  > pullz_umbr_23.xvg:
>  > 0.  6.09702 0.0233141
>  >
>  > pullz_umbr_50.xvg:
>  > 0.  6.02097 -2.50088
>  >
>  > g_wham command:
>  > g_wham -b 5000 -it tpr_files.dat  -ix pullz_files.dat -o
>  > profile_test.xvg -hist histo_test.xvg  -unit kCal
>  >
>  > My pull code:
>  >
>  > pull= umbrella
>  > pull_geometry   = distance
>  > pull_dim= N N Y
>  > pull_start  = yes
>  > pull_ngroups= 1
>  > pull_group0 = POPC_POPS ; reference group is bilayer
>  > pull_group1 = C-alpha_&_r_92-94 ; group that is actually

pulled

>  > pull_init1  = 0
>  > pull_rate1  = 0.0
>  > pull_k1 = 1000 ; kJ mol-1 nm-2
>  >
>
> Your problem stems from the use of "distance" geometry.  This

method

> assumes the
> sign along the reaction coordinate does not change, i.e. always
> positive or
> always negative.  If the sign changes, this simple method fails.
>  You should be
> using something like "position" to allow for a vector to be
> specified.  Perhaps
> you can reconstruct the PMF by separately analyzing the positive
> restraint
> distances and negative restraint distances (note here that
> "distance" really
> refers to a vector quantity, and thus it can have a sign), or
> otherwise create
> new .tpr files using "position" geometry, though I don't know if
> g_wham will
> accept them or not.
>
> -Justin
>
> --
> 
>
> 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
>
> 
>
>
> Thank's!
>
> I managed to solve my g_wham problem by doing two things:
>
> 1. New tpr-files with proper pull code for g_wham.
> 2. I also needed to modify signs of pullf values: If value for pullx
> distance was negative, I reversed the sign of corresponding pullf

value.

> I did that by my own script.
>
> The new pull code:
>
> ; Pull code
>
> pull= umbrella
> pull_geometry   = direction
> pull_vec1   = 0 0 1
> pull_start  = yes
> pull_ngroups= 1
> pull_group0 = POPC_POPS ; reference group is bilayer
> pull_group1 = C-alpha_&_r_92-94 ; group that is actually pulled
> pull_init1  = 0
> pull_rate1  = 0.0
> pull_k1 = 1000 ; kJ mol-1 nm-2
>
> I am little bit confuced, why I needed to tweak signes of pullf

values.

> But like that I got the curve that resembles two half curve made for
> positive and negative pullx distances separately. That curve also

makes

> sense from biochemical point of view.
>
Such changes do not seem appropriate to me.  If you change the sign of
the
pulling force, you change the implication of what that value means.
What
happens if you run your simulations with the new (more appropriate)
.mdp file?
Do the forces have the same magnitude, but opposite sign?


I don't think that the problem is so easy fixed. I had with another
person about a month ago a lengthy discussion on the list.

The problem is the following:
If you use 'distance' as pull_geometry the position of the minimum of
the umbrella potential is determined by 

Re: [gmx-users] File editing - only one layer of water around a molecule

[Lara Bunte]

Hi Justin

Okay, after 


g_select -f mol_in_water.pdb -select '"Close to ISO" resname SOL and within 0.5 
of group "ISO"'


I got:

selection parser: invalid selection '"Close to ISO" resname SOL and within 0.5 
of group "ISO"'

Input error or input inconsistency:
selection(s) could not be parsed


I also tried other permutations of ISO and SOL and got the same. 


I read the complete help to g_select twice and I understand nothing what there 
is written.  In general I like Gromacs more and more but g_select program is 
totally fucked. I don't get it. :-(

Greetings
Lara

p.s.
Here in this email if I got to answer (like always) is only Justins mail 
adress, not the gromacs user list. I do it in cc








 Von: Justin A. Lemkul 
An: Lara Bunte ; Discussion list for GROMACS users 
 
Gesendet: 14:59 Freitag, 13.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a 
molecule
 


Lara Bunte wrote:
> Hi
> 
> I tried but I got an error. In my mol_in_water.pdb file all atoms of my 
> molecule has the group notation ISO and all the water atoms has the group 
> notation SOL. I used following command:
> 
> g_select -f my mol_in_water.pdb -other -options -select '"Close to ISO" 
> resname SOL and within 0.5 of group "ISO"'
> 
> and I got the error:
> 
> Invalid command line argument:
> -other
> 
> How can I fix it.
> 

Please see g_select -h for valid options.  Mark was simply implying that you 
will likely need other command line options to make the program actually do 
something.  Also note the space in your "my mol_in_water.pdb" will cause 
problems as well.

-Justin

-- 

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

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Re: [gmx-users] File editing - only one layer of water around a molecule

[Justin A. Lemkul]

Lara Bunte wrote:

Hi

I tried but I got an error. In my mol_in_water.pdb file all atoms of my 
molecule has the group notation ISO and all the water atoms has the 
group notation SOL. I used following command:


g_select -f my mol_in_water.pdb -other -options -select '"Close to ISO" 
resname SOL and within 0.5 of group "ISO"'


and I got the error:

Invalid command line argument:
-other

How can I fix it.



Please see g_select -h for valid options.  Mark was simply implying that you 
will likely need other command line options to make the program actually do 
something.  Also note the space in your "my mol_in_water.pdb" will cause 
problems as well.


-Justin

--


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


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Re: [gmx-users] File editing - only one layer of water around a molecule

[Lara Bunte]

Hi

I tried but I got an error. In my mol_in_water.pdb file all atoms of my 
molecule has the group notation ISO and all the water atoms has the group 
notation SOL. I used following command:

g_select -f my mol_in_water.pdb -other -options -select '"Close to ISO" resname 
SOL and within 0.5 of group "ISO"'


and I got the error:

Invalid command line argument:
-other


How can I fix it.


Greetings
Lara







 Von: Mark Abraham 
An: Discussion list for GROMACS users  
Gesendet: 12:23 Freitag, 13.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a 
molecule
 

On 13/04/2012 8:17 PM, Lara Bunte wrote: 
Thanks for that but where in this do I give Gromacs my pdb. file. From where do 
g_select use this information? 
>
>
>
>What I have is a pdb file. 
>
Look at g_select -h for -f and -s. Like every GROMACS tool, .pdb is
one of the file types you can use instead of a trajectory or run
input file in cases where (as here) that makes sense.

On a more general note, I hope you've done all the GROMACS tutorial
material you can find - this question is one example of the kind of
usage "general knowledge" that can often be acquired that way.

Mark



>
>Greetings
>Lara
>
>
>
>
>
>
>
> Von: Mark Abraham 
>An: Discussion list for GROMACS users  
>Gesendet: 12:06 Freitag, 13.April 2012
>Betreff: Re: [gmx-users] File editing - only one layer of water around a 
>molecule
> 
>
>On 13/04/2012 8:01 PM, Lara Bunte wrote: 
>Hi Mark
>>
>>
>>Could you please give me for that the prompt how to write this in the 
>>console. 
>>
>>
>>
>>"All atoms of a residue LIG within 0.5 nm of a protein (with a custom name):
>>  "Close to protein" resname LIG and within 0.5 of
  group "Protein" "
>>
>>
>>
>>So how to put this into the console? I often found in the manual text that I 
>>don't know how to concretely type in into the bash console? 
>>
>>
>>
>>Thanks for helping me and sorry for my questions. I am a noob :-( 
>>
>The text for g_select -h in the upcoming GROMACS release
will make this clearer, as others have struggled with
this part recently.
>
>g_select -other -options -select '"Close to protein"
resname LIG and within 0.5 of group "Protein"'
>
>works for that example. Note carefully the use of single
and double quotes.
>
>Mark
>
>
>
>>
>>Greetings
>>Lara
>>
>>
>>
>>
>>
>>
>>
>>
>> Von: Mark Abraham 
>>An: Discussion list for GROMACS users  
>>Gesendet: 11:51 Freitag, 13.April 2012
>>Betreff: Re: [gmx-users] File editing - only one layer of water around a 
>>molecule
>> 
>>
>>On 13/04/2012 7:29 PM, Lara Bunte wrote: 
>>I read g_select -select 'help all' and I understand nothing of that. 
>>>
>>>
>>>
>>>In general one have a molecule (valences closed by hydrogen) and a water box 
>>>around it. How to select only the protein with the first water layers, say 
>>>one layer? 
>>>
>>>
>>>Please give me an example how to do this with gromacs. I read the examples 
>>>in g_select -select 'help all' and I have no Idea what they are talking 
>>>about. 
>>>
>>Surely you can see that the example
>>
>>All atoms of a residue LIG within 0.5 nm of
a protein (with a custom name):
>>  "Close to protein" resname LIG and within
0.5 of group "Protein" 
>>
>>is very similar to what would be needed for
all water residues within some distance of
your solute.
>>
>>VMD uses a similar approach. BioPython
probably likewise. There's no genie going to
wave the magic create-a-layer wand. You need
to learn how to create a layer from a
definition that suits you, because you'll
probably have to vary that definition until
you're happy with the outcome.
>>
>>Mark
>>
>>
>>
>>>
>>>Thanks for help
>>>Greetings
>>>Lara
>>>
>>>
>>>
>>> 
>>>
>>>
>>>
>>>
>>> Von: Mark Abraham 
>>>An: Discussion list for GROMACS users  
>>>Gesendet: 19:26 Mittwoch, 11.April 2012
>>>Betreff: Re: [gmx-users] File editing - only one layer of water around a 
>>>molecule
>>> 
>>>On 12/04/2012 3:24 AM, Justin A.
Lemkul wrote:
 
 
 Lara Bunte wrote:
> Could you please give how
g_select is used?
>>>
>>>Reading g_select -h might have led
you to try g_select -select 'help'
>>>
> Is there a tutorial for
that?
> 
 
 g_select -select 'help all'
 
 The information contained
therein is very extensive, so be
sure to read it thoro

[gmx-users] Re: Pull code: separating molecules. distance and direction (SOLVED)

[Eudes Fileti]

Hello, I found out where my mistake.
pull_dim is Y Y Y and not N N Y.

Bests
eef
___
Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Rua Talim, 330, São José dos Campos - SP
Tel.: (12) 3309-9573
Página: sites.google.com/site/fileti/



On 11 April 2012 10:28, Eudes Fileti  wrote:

> Hello everybody, I have used pull code to separate two molecules in water.
> The idea is to generate initial configurations for umbrella sampling.
> Initially I tried to use pull_geometry=distance. I noticed that the vector
> connecting
> the two molecules are not remained on the main axis of the box (z). Then I
> realized
> that using pull_geometry=direction (with pull_vec1= 0 0 1) I could keep
> this distance
> on the z axis. However, the result of the pulling was exactly the same as
> with
> pull_geometry=distance, ie, as the molecule moves away from the reference
> molecule the
> distance of separation does not remain on the z axis, as I wish.
>
> The protocol used was as follows:
> pull = umbrella
> pull_geometry= direction
> pull_dim = N N Y
> pull_ngroups = 1
> pull_group0  = mol_0
> pull_weights0=
> pull_pbcatom0= 0
> pull_group1  = mol_1
> pull_weights1=
> pull_pbcatom1= 0
> pull_vec1= 0.0 0.0 1.0
> pull_init1   = 0.0
> pull_rate1   = 0.01
> pull_k1  = 1000
>
> Someone could direct me to where I am wrong?
> Bests
> eef
> ___
> Eudes Eterno Fileti
> Instituto de Ciência e Tecnologia da UNIFESP
> Rua Talim, 330, São José dos Campos - SP
> Tel.: (12) 3309-9573
> Página: sites.google.com/site/fileti/
>
>
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[gmx-users] a question related to production MD

[Acoot Brett]

Dear All,


Before we run the production MD, we have minimized the energy and equilibriated 
the system. Especially we will keep the temperature constant. Then which force 
drive the protein to converge? Why the protein do not reverse its already 
completed MD process before it converges, leading to that the system will never 
converge? Which computation technique is adopted so that the production MD will 
be in the process of converging?

Cheers,

Acoot-- 
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Re: [gmx-users] g_wham problem with negative COM differences

[Justin A. Lemkul]

Anni Kauko wrote:


Date: Wed, 11 Apr 2012 08:38:05 -0400
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] g_wham problem with negative COM differences
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID: <4f857b2d.3050...@vt.edu >
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Anni Kauko wrote:
 > Hi!
 >
 > I try to perform pmf calculations for case where a peptide shifts
 > through the membrane. My COM differences should vary from 2.3 to
-2.5.
 >
 > My problem is that g_wham plots negative COM difference as they
would be
 > positive.  In pullx-files the COM differences are treated correctly
 > (look below). My peptide is not symmetric, so profile curves are not
 > symmetric, so loosing the sign for COM difference screws my profile
 > curve completely.
 >
 > I did not manage to find any pre-existing answers to this problem
from
 > internet.
 >
 > First datalines from pullx files:
 > (sorry for strange file names...)
 >
 > pull_umbr_0.xvg:
 > 0.  6.26031 2.27369
 >
 > pullz_umbr_23.xvg:
 > 0.  6.09702 0.0233141
 >
 > pullz_umbr_50.xvg:
 > 0.  6.02097 -2.50088
 >
 > g_wham command:
 > g_wham -b 5000 -it tpr_files.dat  -ix pullz_files.dat -o
 > profile_test.xvg -hist histo_test.xvg  -unit kCal
 >
 > My pull code:
 >
 > pull= umbrella
 > pull_geometry   = distance
 > pull_dim= N N Y
 > pull_start  = yes
 > pull_ngroups= 1
 > pull_group0 = POPC_POPS ; reference group is bilayer
 > pull_group1 = C-alpha_&_r_92-94 ; group that is actually pulled
 > pull_init1  = 0
 > pull_rate1  = 0.0
 > pull_k1 = 1000 ; kJ mol^-1 nm^-2
 >

Your problem stems from the use of "distance" geometry.  This method
assumes the
sign along the reaction coordinate does not change, i.e. always
positive or
always negative.  If the sign changes, this simple method fails.
 You should be
using something like "position" to allow for a vector to be
specified.  Perhaps
you can reconstruct the PMF by separately analyzing the positive
restraint
distances and negative restraint distances (note here that
"distance" really
refers to a vector quantity, and thus it can have a sign), or
otherwise create
new .tpr files using "position" geometry, though I don't know if
g_wham will
accept them or not.

-Justin

--


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




Thank's!

I managed to solve my g_wham problem by doing two things:

1. New tpr-files with proper pull code for g_wham.
2. I also needed to modify signs of pullf values: If value for pullx 
distance was negative, I reversed the sign of corresponding pullf value. 
I did that by my own script.


The new pull code:

; Pull code

pull= umbrella
pull_geometry   = direction
pull_vec1   = 0 0 1
pull_start  = yes
pull_ngroups= 1
pull_group0 = POPC_POPS ; reference group is bilayer
pull_group1 = C-alpha_&_r_92-94 ; group that is actually pulled
pull_init1  = 0
pull_rate1  = 0.0
pull_k1 = 1000 ; kJ mol^-1 nm^-2
   
I am little bit confuced, why I needed to tweak signes of pullf values. 
But like that I got the curve that resembles two half curve made for 
positive and negative pullx distances separately. That curve also makes 
sense from biochemical point of view.




Such changes do not seem appropriate to me.  If you change the sign of the 
pulling force, you change the implication of what that value means.  What 
happens if you run your simulations with the new (more appropriate) .mdp file? 
Do the forces have the same magnitude, but opposite sign?



-Anni

PS. Thank's for your excellent tutorials. They have been indispensable 
help for me to get started with gromacs!


Glad to hear it :)

-Justin

--


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


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ww

Re: [gmx-users] Simulation of the pure lipid bilayer

[Justin A. Lemkul]

rajat desikan wrote:
Justin,I have a question. If we download files from Peter Tieleman's 
website, all you get are .gro files, and no cpt files. Then what should 
one do? Continue using the velocities in the .gro file?




Run a new equilibration.  IIRC, those structures are the product of very short 
(2 ns or so) simulations produced many years ago.  More equilibration is 
expected for more modern simulations.


-Justin

On Fri, Apr 13, 2012 at 5:28 PM, Justin A. Lemkul > wrote:




James Starlight wrote:

Dear Gromacs Users!


I want to perform simulation of the pure bilayer surrounded by
water. I'm using already pre-equilibrated bilayers as the
initial structure. During conversion pdb-> gro -> pdb the
velocities from initial equilibration runs of the structure were
lost. Should I start generating


Relying on a .gro file to maintain velocities is a bad idea.  The
values contained therein lack sufficient precision to be reliable.
 You should be using .cpt files to continue runs to preserve the
previous ensemble, thus making the choice of coordinate file format
irrelevant.

this velocities in my production run ( gen_Vel= yes) or i must
do equilibration instead first to generate velocities? Finally
what length


A production run should not start with newly generated velocities.
 Doing so destroys the initial equilibration, and if you haven't
taken care to preserve that anyway, you should probably just start
over and make proper use of .cpt files.

should this equilibration be to provide reasonable velocities
for futrher MD run if I would avoild long equilibration period
because of suitability of my initial model?


There is no universal answer to this question.  It depends on your
criteria for convergence and contents of the system, among other
considerations.

-Justin

-- 
==__==


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
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--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore


--


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


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Re: [gmx-users] Simulation of the pure lipid bilayer

[rajat desikan]

Justin,I have a question. If we download files from Peter Tieleman's
website, all you get are .gro files, and no cpt files. Then what should one
do? Continue using the velocities in the .gro file?

On Fri, Apr 13, 2012 at 5:28 PM, Justin A. Lemkul  wrote:

>
>
> James Starlight wrote:
>
>> Dear Gromacs Users!
>>
>>
>> I want to perform simulation of the pure bilayer surrounded by water. I'm
>> using already pre-equilibrated bilayers as the initial structure. During
>> conversion pdb-> gro -> pdb the velocities from initial equilibration runs
>> of the structure were lost. Should I start generating
>>
>
> Relying on a .gro file to maintain velocities is a bad idea.  The values
> contained therein lack sufficient precision to be reliable.  You should be
> using .cpt files to continue runs to preserve the previous ensemble, thus
> making the choice of coordinate file format irrelevant.
>
>  this velocities in my production run ( gen_Vel= yes) or i must do
>> equilibration instead first to generate velocities? Finally what length
>>
>
> A production run should not start with newly generated velocities.  Doing
> so destroys the initial equilibration, and if you haven't taken care to
> preserve that anyway, you should probably just start over and make proper
> use of .cpt files.
>
>  should this equilibration be to provide reasonable velocities for futrher
>> MD run if I would avoild long equilibration period because of suitability
>> of my initial model?
>>
>>
> There is no universal answer to this question.  It depends on your
> criteria for convergence and contents of the system, among other
> considerations.
>
> -Justin
>
> --
> ==**==
>
> 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
>
> ==**==
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] a question related to NMR

[Justin A. Lemkul]

Acoot Brett wrote:

Dear All,
 
Before we run the production MD, we have minimized the energy and 
equilibriated the system. Especially we will keep the temperature 
constant. Then which force drive the protein to converge? Why the 
protein do not reverse its already completed MD process before it 
converges, leading to that the system will never converge? Which 
computation technique is adopted so that the production MD will be in 
the process of converging?
 


Do not assume that a converged simulation necessarily produces one "correct" 
structure.  A converged simulation will still move over time, but the ensemble 
of structures that it samples does not change.  For instance, you'll never get a 
protein to stay put.  It will wiggle around within a defined set of 
configurations that define its stability and inherent dynamics.  The time over 
which this takes to occur depends on a lot of factors and cannot be easily 
generalized.  There is no special technique to force a simulation to converge, 
you just have to wait.


-Justin

--


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


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Re: [gmx-users] Simulation of the pure lipid bilayer

[Justin A. Lemkul]

James Starlight wrote:

Dear Gromacs Users!


I want to perform simulation of the pure bilayer surrounded by water. 
I'm using already pre-equilibrated bilayers as the initial structure. 
During conversion pdb-> gro -> pdb the velocities from initial 
equilibration runs of the structure were lost. Should I start generating 


Relying on a .gro file to maintain velocities is a bad idea.  The values 
contained therein lack sufficient precision to be reliable.  You should be using 
.cpt files to continue runs to preserve the previous ensemble, thus making the 
choice of coordinate file format irrelevant.


this velocities in my production run ( gen_Vel= yes) or i must do 
equilibration instead first to generate velocities? Finally what length 


A production run should not start with newly generated velocities.  Doing so 
destroys the initial equilibration, and if you haven't taken care to preserve 
that anyway, you should probably just start over and make proper use of .cpt files.


should this equilibration be to provide reasonable velocities for 
futrher MD run if I would avoild long equilibration period because of 
suitability of my initial model?




There is no universal answer to this question.  It depends on your criteria for 
convergence and contents of the system, among other considerations.


-Justin

--


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


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Re: [gmx-users] -rcon parameter in mdrun - what values have sense?

[Justin A. Lemkul]

Иимяа Фаамиилиияа wrote:

Hi,

I constructed some (about 200 atoms) molecule, have got itp and gro files for it using PRODRG 
server and put it in water box.


Is the topology just the raw output from PRODRG?  The parameters are often of 
poor quality and lead to unreliable simulations.  See, for instance:


http://pubs.acs.org/doi/abs/10.1021/ci100335w

I have occasionally observed complete crashes when using PRODRG parameters.


Short test run was O'K. But when I tried long run I have got message:
after about 1.5ns time: 
--

DD cell 0 1 0: Neighboring cells do not have atoms: 73
DD cell 0 3 0: Neighboring cells do not have atoms: 50 49

Program mdrun, VERSION 4.5.5
Source code file: domdec_con.c, line: 693

Fatal error:
DD cell 0 1 0 could only obtain 43 of the 44 atoms that are connected via constraints 
from the neighboring cells. This probably means your constraint lengths are too long 
compared to the domain decomposition cell size. Decrease the number of domain 
decomposition grid cells or lincs-order or use the -rcon option of mdrun. For more 
information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors
--- 
I do not know where I can 
1) "...decrease the number of domain 
decomposition grid cells or 


Use fewer threads/processors.


2) decrease lincs-order".



This is specified in the .mdp file, but is likely not necessary.


3) I can use  -rcon option of mdrun.
In this case I understand how I can change this parameter but I don't know what 
are the reasonable values for it.
Is it 0.761A  at the beginning of my calculation (see below)? 
Should I try to make it shorter or longer?

It looks that from one hand I should make it longer but from another hand it 
should be less
than minimum cell size (0.898 in my case? see below)  



I doubt you should be messing with these settings.  Your simulation appears to 
be crashing.  My first suspect is the topology from PRODRG, though in the 
absence of a complete .mdp file and description of the system, that's just 
conjecture at the moment.  See also:


http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin


I have next information about domain decomposition in the beginning of run:
- 
Initializing Domain Decomposition on 64 nodes

Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.817 nm, LJ-14, atoms 138 148
  multi-body bonded interactions: 0.817 nm, Proper Dih., atoms 148 138
Minimum cell size due to bonded interactions: 0.898 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.761 nm
Estimated maximum distance required for P-LINCS: 0.761 nm
Using 32 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 32 cells with a minimum initial size of 1.123 nm
The maximum allowed number of cells is: X 5 Y 5 Z 5
Domain decomposition grid 4 x 4 x 2, separate PME nodes 32
PME domain decomposition: 4 x 8 x 1
Interleaving PP and PME nodes
This is a particle-particle only node
-


Any ideas what to do?
Thank you in advance.
Alex









--


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


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[gmx-users] -rcon parameter in mdrun - what values have sense?

[Иимяа Фаамиилиияа]

Hi,

I constructed some (about 200 atoms) molecule, have got itp and gro files for 
it using PRODRG 
server and put it in water box.
Short test run was O'K. But when I tried long run I have got message:
after about 1.5ns time: 
--
DD cell 0 1 0: Neighboring cells do not have atoms: 73
DD cell 0 3 0: Neighboring cells do not have atoms: 50 49

Program mdrun, VERSION 4.5.5
Source code file: domdec_con.c, line: 693

Fatal error:
DD cell 0 1 0 could only obtain 43 of the 44 atoms that are connected via 
constraints 
from the neighboring cells. This probably means your constraint lengths are too 
long 
compared to the domain decomposition cell size. Decrease the number of domain 
decomposition grid cells or lincs-order or use the -rcon option of mdrun. For 
more 
information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
 
I do not know where I can 
1) "...decrease the number of domain 
decomposition grid cells or 
2) decrease lincs-order".

3) I can use  -rcon option of mdrun.
In this case I understand how I can change this parameter but I don't know what 
are the reasonable values for it.
Is it 0.761A  at the beginning of my calculation (see below)? 
Should I try to make it shorter or longer?
It looks that from one hand I should make it longer but from another hand it 
should be less
than minimum cell size (0.898 in my case? see below)  

I have next information about domain decomposition in the beginning of run:
-
 
Initializing Domain Decomposition on 64 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.817 nm, LJ-14, atoms 138 148
  multi-body bonded interactions: 0.817 nm, Proper Dih., atoms 148 138
Minimum cell size due to bonded interactions: 0.898 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.761 nm
Estimated maximum distance required for P-LINCS: 0.761 nm
Using 32 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 32 cells with a minimum initial size of 1.123 nm
The maximum allowed number of cells is: X 5 Y 5 Z 5
Domain decomposition grid 4 x 4 x 2, separate PME nodes 32
PME domain decomposition: 4 x 8 x 1
Interleaving PP and PME nodes
This is a particle-particle only node
-


Any ideas what to do?
Thank you in advance.
Alex





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[gmx-users] oscillational period problem in Martini force field

[Du Jiangfeng (BIOCH)]

Dear Friends,

I am doing MD simulation to a coarse grained system by using martini force 
field. According to Martini recommendation, the MD time step should be in 20-40 
fs. 
Since I selected 20 fs, the warning comes: "estimated oscillational period is 
less than 5 times of the time step".
I could erase the warning by decreasing the time step to 8 fs, which is not 
recommended by Martini force field. 

Here is my question: Should I ignore this warning or decrease time step or 
struggle with the protein system (the system seems not to be improved any more) 
?

Any reply would be appreciated,

Thank you

Jiangfeng Du, PhD Student
Cardiovascular Research Institute Maastricht
Department of Biochemistry
P.O. Box 616
Mobile: +31-681741859
FAX: +31-43-3884159
6200 MD Maastricht
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[gmx-users] a question related to NMR

[Acoot Brett]

Dear All,
 
Before we run the production MD, we have minimized the energy and equilibriated 
the system. Especially we will keep the temperature constant. Then which force 
drive the protein to converge? Why the protein do not reverse its already 
completed MD process before it converges, leading to that the system will never 
converge? Which computation technique is adopted so that the production MD will 
be in the process of converging?
 
Cheers,
 
Acoot-- 
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Re: [gmx-users] Box Size in MD

[Mark Abraham]

On 13/04/2012 8:12 PM, Lara Bunte wrote:

Hi Justin

What is a box vector?


See manual 3.2. See tutorial material for different ways of making boxes.

I read that the CHARMM force field that I am using has a cut-off of 1 
(is this Angstrom or nano-meters?).


That's a totally separate concept, but can contribute to the box size 
decision. Probably that source meant 1nm, since a cutoff that is shorter 
than a C-C bond would be pretty useless as a model. Never just take a 
number out of context or without dimensions, or you'll curse yourself later.



So should I use a box size of 3 nano-meters?


We can't tell on the information you've given - and you should decide 
for yourself after familiarizing yourself with GROMACS workflows and 
thinking about what you need for your simulation, and comparing your 
proposed setup with what others have done in published work.


Mark



Greetings
Lara



*Von:* Justin A. Lemkul 
*An:* Lara Bunte ; Discussion list for GROMACS 
users 

*Gesendet:* 17:28 Donnerstag, 22.März 2012
*Betreff:* Re: [gmx-users] Box Size in MD



Lara Bunte wrote:
> Hello
>
> What size should a box have in that you do your MD? I always read 
that for
> short Lennard Jones interactions one should do a cut off with the 
half of the

> box size but what how to know a good box size?
>

This is not correct.  The cutoffs are dictated by the force field 
you've chosen to use.  There are predefined values that should (for 
the most part) be adhered to.  What you need to make sure of when 
setting up the box is that the longest cutoff cannot exceed half the 
shortest box vector.  If it does, you get duplicate force evaluations 
from a violation of the minimum image convention. Use of an NPT 
ensemble will cause the box dimensions to fluctuate (due to pressure) 
and thus it is unwise in such cases to ever have a box that is only 
twice the size of the longest cutoff, as violations are almost certain 
to occur.


-Justin

-- 

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








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Re: [gmx-users] File editing - only one layer of water around a molecule

[Mark Abraham]

On 13/04/2012 8:17 PM, Lara Bunte wrote:
Thanks for that but where in this do I give Gromacs my pdb. file. From 
where do g_select use this information?


What I have is a pdb file.


Look at g_select -h for -f and -s. Like every GROMACS tool, .pdb is one 
of the file types you can use instead of a trajectory or run input file 
in cases where (as here) that makes sense.


On a more general note, I hope you've done all the GROMACS tutorial 
material you can find - this question is one example of the kind of 
usage "general knowledge" that can often be acquired that way.


Mark



Greetings
Lara



*Von:* Mark Abraham 
*An:* Discussion list for GROMACS users 
*Gesendet:* 12:06 Freitag, 13.April 2012
*Betreff:* Re: [gmx-users] File editing - only one layer of water 
around a molecule


On 13/04/2012 8:01 PM, Lara Bunte wrote:

Hi Mark

Could you please give me for that the prompt how to write this in the 
console.


"All atoms of a residue LIG within 0.5 nm of a protein (with a custom 
name):

  "Close to protein" resname LIG and within 0.5 of group "Protein" "

So how to put this into the console? I often found in the manual text 
that I don't know how to concretely type in into the bash console?


Thanks for helping me and sorry for my questions. I am a noob :-(


The text for g_select -h in the upcoming GROMACS release will make 
this clearer, as others have struggled with this part recently.


g_select -other -options -select '"Close to protein" resname LIG and 
within 0.5 of group "Protein"'


works for that example. Note carefully the use of single and double 
quotes.


Mark



Greetings
Lara




*Von:* Mark Abraham  

*An:* Discussion list for GROMACS users  


*Gesendet:* 11:51 Freitag, 13.April 2012
*Betreff:* Re: [gmx-users] File editing - only one layer of water 
around a molecule


On 13/04/2012 7:29 PM, Lara Bunte wrote:

I read g_select -select 'help all' and I understand nothing of that.

In general one have a molecule (valences closed by hydrogen) and a 
water box around it. How to select only the protein with the first 
water layers, say one layer?


Please give me an example how to do this with gromacs. I read the 
examples in g_select -select 'help all' and I have no Idea what they 
are talking about.


Surely you can see that the example

All atoms of a residue LIG within 0.5 nm of a protein (with a custom 
name):

  "Close to protein" resname LIG and within 0.5 of group "Protein"

is very similar to what would be needed for all water residues within 
some distance of your solute.


VMD uses a similar approach. BioPython probably likewise. There's no 
genie going to wave the magic create-a-layer wand. You need to learn 
how to create a layer from a definition that suits you, because 
you'll probably have to vary that definition until you're happy with 
the outcome.


Mark



Thanks for help
Greetings
Lara




*Von:* Mark Abraham  

*An:* Discussion list for GROMACS users  


*Gesendet:* 19:26 Mittwoch, 11.April 2012
*Betreff:* Re: [gmx-users] File editing - only one layer of water 
around a molecule


On 12/04/2012 3:24 AM, Justin A. Lemkul wrote:
>
>
> Lara Bunte wrote:
>> Could you please give how g_select is used?

Reading g_select -h might have led you to try g_select -select 'help'

>> Is there a tutorial for that?
>>
>
> g_select -select 'help all'
>
> The information contained therein is very extensive, so be sure to 
read it thoroughly.  It will fill several terminal windows 
explaining the syntax and providing examples.


... and search Google for some examples.

Mark
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Re: [gmx-users] File editing - only one layer of water around a molecule

[Lara Bunte]

Thanks for that but where in this do I give Gromacs my pdb. file. From where do 
g_select use this information? 


What I have is a pdb file. 


Greetings
Lara






 Von: Mark Abraham 
An: Discussion list for GROMACS users  
Gesendet: 12:06 Freitag, 13.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a 
molecule
 

On 13/04/2012 8:01 PM, Lara Bunte wrote: 
Hi Mark
>
>
>Could you please give me for that the prompt how to write this in the console. 
>
>
>
>"All atoms of a residue LIG within 0.5 nm of a protein (with a custom name):
>  "Close to protein" resname LIG and within 0.5 of group
  "Protein" "
>
>
>
>So how to put this into the console? I often found in the manual text that I 
>don't know how to concretely type in into the bash console? 
>
>
>
>Thanks for helping me and sorry for my questions. I am a noob :-( 
>
The text for g_select -h in the upcoming GROMACS release will make
this clearer, as others have struggled with this part recently.

g_select -other -options -select '"Close to protein" resname LIG and
within 0.5 of group "Protein"'

works for that example. Note carefully the use of single and double
quotes.

Mark



>
>Greetings
>Lara
>
>
>
>
>
>
>
>
> Von: Mark Abraham 
>An: Discussion list for GROMACS users  
>Gesendet: 11:51 Freitag, 13.April 2012
>Betreff: Re: [gmx-users] File editing - only one layer of water around a 
>molecule
> 
>
>On 13/04/2012 7:29 PM, Lara Bunte wrote: 
>I read g_select -select 'help all' and I understand nothing of that. 
>>
>>
>>
>>In general one have a molecule (valences closed by hydrogen) and a water box 
>>around it. How to select only the protein with the first water layers, say 
>>one layer? 
>>
>>
>>Please give me an example how to do this with gromacs. I read the examples in 
>>g_select -select 'help all' and I have no Idea what they are talking about. 
>>
>Surely you can see that the example
>
>All atoms of a residue LIG within 0.5 nm of a protein
(with a custom name):
>  "Close to protein" resname LIG and within 0.5 of group
"Protein" 
>
>is very similar to what would be needed for all water
residues within some distance of your solute.
>
>VMD uses a similar approach. BioPython probably
likewise. There's no genie going to wave the magic
create-a-layer wand. You need to learn how to create a
layer from a definition that suits you, because you'll
probably have to vary that definition until you're happy
with the outcome.
>
>Mark
>
>
>
>>
>>Thanks for help
>>Greetings
>>Lara
>>
>>
>>
>> 
>>
>>
>>
>>
>> Von: Mark Abraham 
>>An: Discussion list for GROMACS users  
>>Gesendet: 19:26 Mittwoch, 11.April 2012
>>Betreff: Re: [gmx-users] File editing - only one layer of water around a 
>>molecule
>> 
>>On 12/04/2012 3:24 AM, Justin A. Lemkul wrote:
>>> 
>>> 
>>> Lara Bunte wrote:
 Could you please give how g_select is
used?
>>
>>Reading g_select -h might have led you to try
g_select -select 'help'
>>
 Is there a tutorial for that?
 
>>> 
>>> g_select -select 'help all'
>>> 
>>> The information contained therein is very
extensive, so be sure to read it thoroughly.  It
will fill several terminal windows explaining
the syntax and providing examples.
>>
>>... and search Google for some examples.
>>
>>Mark
>>-- gmx-users mailing list    gmx-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] Box Size in MD

[Lara Bunte]

Hi Justin

What is a box vector? I read that the CHARMM force field that I am using has a 
cut-off of 1 (is this Angstrom or nano-meters?). So should I use a box size of 
3 nano-meters? 


Greetings
Lara





 Von: Justin A. Lemkul 
An: Lara Bunte ; Discussion list for GROMACS users 
 
Gesendet: 17:28 Donnerstag, 22.März 2012
Betreff: Re: [gmx-users] Box Size in MD
 


Lara Bunte wrote:
> Hello
> 
> What size should a box have in that you do your MD? I always read that for
> short Lennard Jones interactions one should do a cut off with the half of the
> box size but what how to know a good box size?
> 

This is not correct.  The cutoffs are dictated by the force field you've chosen 
to use.  There are predefined values that should (for the most part) be adhered 
to.  What you need to make sure of when setting up the box is that the longest 
cutoff cannot exceed half the shortest box vector.  If it does, you get 
duplicate force evaluations from a violation of the minimum image convention. 
Use of an NPT ensemble will cause the box dimensions to fluctuate (due to 
pressure) and thus it is unwise in such cases to ever have a box that is only 
twice the size of the longest cutoff, as violations are almost certain to occur.

-Justin

-- 

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

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Re: [gmx-users] File editing - only one layer of water around a molecule

[Mark Abraham]

On 13/04/2012 8:01 PM, Lara Bunte wrote:

Hi Mark

Could you please give me for that the prompt how to write this in the 
console.


"All atoms of a residue LIG within 0.5 nm of a protein (with a custom 
name):

  "Close to protein" resname LIG and within 0.5 of group "Protein" "

So how to put this into the console? I often found in the manual text 
that I don't know how to concretely type in into the bash console?


Thanks for helping me and sorry for my questions. I am a noob :-(


The text for g_select -h in the upcoming GROMACS release will make this 
clearer, as others have struggled with this part recently.


g_select -other -options -select '"Close to protein" resname LIG and 
within 0.5 of group "Protein"'


works for that example. Note carefully the use of single and double quotes.

Mark



Greetings
Lara




*Von:* Mark Abraham 
*An:* Discussion list for GROMACS users 
*Gesendet:* 11:51 Freitag, 13.April 2012
*Betreff:* Re: [gmx-users] File editing - only one layer of water 
around a molecule


On 13/04/2012 7:29 PM, Lara Bunte wrote:

I read g_select -select 'help all' and I understand nothing of that.

In general one have a molecule (valences closed by hydrogen) and a 
water box around it. How to select only the protein with the first 
water layers, say one layer?


Please give me an example how to do this with gromacs. I read the 
examples in g_select -select 'help all' and I have no Idea what they 
are talking about.


Surely you can see that the example

All atoms of a residue LIG within 0.5 nm of a protein (with a custom 
name):

  "Close to protein" resname LIG and within 0.5 of group "Protein"

is very similar to what would be needed for all water residues within 
some distance of your solute.


VMD uses a similar approach. BioPython probably likewise. There's no 
genie going to wave the magic create-a-layer wand. You need to learn 
how to create a layer from a definition that suits you, because you'll 
probably have to vary that definition until you're happy with the outcome.


Mark



Thanks for help
Greetings
Lara




*Von:* Mark Abraham  

*An:* Discussion list for GROMACS users  


*Gesendet:* 19:26 Mittwoch, 11.April 2012
*Betreff:* Re: [gmx-users] File editing - only one layer of water 
around a molecule


On 12/04/2012 3:24 AM, Justin A. Lemkul wrote:
>
>
> Lara Bunte wrote:
>> Could you please give how g_select is used?

Reading g_select -h might have led you to try g_select -select 'help'

>> Is there a tutorial for that?
>>
>
> g_select -select 'help all'
>
> The information contained therein is very extensive, so be sure to 
read it thoroughly.  It will fill several terminal windows explaining 
the syntax and providing examples.


... and search Google for some examples.

Mark
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Re: [gmx-users] File editing - only one layer of water around a molecule

[Lara Bunte]

Hi Mark

Could you please give me for that the prompt how to write this in the console. 


"All atoms of a residue LIG within 0.5 nm of a protein (with a custom name):
  "Close to protein" resname LIG and within 0.5 of group "Protein" "


So how to put this into the console? I often found in the manual text that I 
don't know how to concretely type in into the bash console? 


Thanks for helping me and sorry for my questions. I am a noob :-(


Greetings
Lara






 Von: Mark Abraham 
An: Discussion list for GROMACS users  
Gesendet: 11:51 Freitag, 13.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a 
molecule
 

On 13/04/2012 7:29 PM, Lara Bunte wrote: 
I read g_select -select 'help all' and I understand nothing of that. 
>
>
>
>In general one have a molecule (valences closed by hydrogen) and a water box 
>around it. How to select only the protein with the first water layers, say one 
>layer? 
>
>
>Please give me an example how to do this with gromacs. I read the examples in 
>g_select -select 'help all' and I have no Idea what they are talking about. 
>
Surely you can see that the example

All atoms of a residue LIG within 0.5 nm of a protein (with a custom
name):
  "Close to protein" resname LIG and within 0.5 of group "Protein" 

is very similar to what would be needed for all water residues
within some distance of your solute.

VMD uses a similar approach. BioPython probably likewise. There's no
genie going to wave the magic create-a-layer wand. You need to learn
how to create a layer from a definition that suits you, because
you'll probably have to vary that definition until you're happy with
the outcome.

Mark



>
>Thanks for help
>Greetings
>Lara
>
>
>
> 
>
>
>
>
> Von: Mark Abraham 
>An: Discussion list for GROMACS users  
>Gesendet: 19:26 Mittwoch, 11.April 2012
>Betreff: Re: [gmx-users] File editing - only one layer of water around a 
>molecule
> 
>On 12/04/2012 3:24 AM, Justin A. Lemkul wrote:
>> 
>> 
>> Lara Bunte wrote:
>>> Could you please give how g_select is used?
>
>Reading g_select -h might have led you to try g_select
-select 'help'
>
>>> Is there a tutorial for that?
>>> 
>> 
>> g_select -select 'help all'
>> 
>> The information contained therein is very extensive, so
be sure to read it thoroughly.  It will fill several
terminal windows explaining the syntax and providing
examples.
>
>... and search Google for some examples.
>
>Mark
>-- gmx-users mailing list    gmx-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] File editing - only one layer of water around a molecule

[Mark Abraham]

On 13/04/2012 7:29 PM, Lara Bunte wrote:

I read g_select -select 'help all' and I understand nothing of that.

In general one have a molecule (valences closed by hydrogen) and a 
water box around it. How to select only the protein with the first 
water layers, say one layer?


Please give me an example how to do this with gromacs. I read the 
examples in g_select -select 'help all' and I have no Idea what they 
are talking about.


Surely you can see that the example

All atoms of a residue LIG within 0.5 nm of a protein (with a custom name):
  "Close to protein" resname LIG and within 0.5 of group "Protein"

is very similar to what would be needed for all water residues within 
some distance of your solute.


VMD uses a similar approach. BioPython probably likewise. There's no 
genie going to wave the magic create-a-layer wand. You need to learn how 
to create a layer from a definition that suits you, because you'll 
probably have to vary that definition until you're happy with the outcome.


Mark



Thanks for help
Greetings
Lara




*Von:* Mark Abraham 
*An:* Discussion list for GROMACS users 
*Gesendet:* 19:26 Mittwoch, 11.April 2012
*Betreff:* Re: [gmx-users] File editing - only one layer of water 
around a molecule


On 12/04/2012 3:24 AM, Justin A. Lemkul wrote:
>
>
> Lara Bunte wrote:
>> Could you please give how g_select is used?

Reading g_select -h might have led you to try g_select -select 'help'

>> Is there a tutorial for that?
>>
>
> g_select -select 'help all'
>
> The information contained therein is very extensive, so be sure to 
read it thoroughly.  It will fill several terminal windows explaining 
the syntax and providing examples.


... and search Google for some examples.

Mark
-- gmx-users mailing list gmx-users@gromacs.org 


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Re: [gmx-users] File editing - only one layer of water around a molecule

[francesco oteri]

Hi Lara, I sent an incomplete mail by error :(

I was saying that the simplest way is using vmd.
Briefly,
1) load the pdb file in vmd.
2) create a representation using a string like:  "same residue as within 3.
of protein".
where "protein" is the group around the molecule you have to use, I
used protein just as example
3. is the cutoff distance between protein and any other ATOM in the
system
3) "same residue" for each atom at point 2) it takes the corresponding
residue avoiding residue bracking.


If your pdb is more complex, but you need only water try:
"water and (same residue as within 3. of protein)".

Now you can visually inspect your selection and adjusting the distance.


When everything is fine, you can save it through vmd save comman:
1) in the command line write:

[atomselect top "same residue as within 3. of protein"] writepdb out.pdb

It should work and it should make the work easier!

Francesco







Il giorno 13 aprile 2012 11:38, francesco oteri
ha scritto:

> Hi Lara,
> the simplest way is using vmd.
> Briefly,
> 1) load the pdb file in vmd.
> 2) create a representation using a string like:  "same residue as within
> 3. of protein".
> where "protein" is the group around the molecule you have to use, I
> used protein just as example
>
>
>
>
> Il giorno 13 aprile 2012 11:29, Lara Bunte  ha
> scritto:
>
> I read g_select -select 'help all' and I understand nothing of that.
>>
>> In general one have a molecule (valences closed by hydrogen) and a water
>> box around it. How to select only the protein with the first water layers,
>> say one layer?
>>
>> Please give me an example how to do this with gromacs. I read the
>> examples in g_select -select 'help all' and I have no Idea what they are
>> talking about.
>>
>> Thanks for help
>> Greetings
>> Lara
>>
>>
>>
>>   --
>> *Von:* Mark Abraham 
>> *An:* Discussion list for GROMACS users 
>> *Gesendet:* 19:26 Mittwoch, 11.April 2012
>>
>> *Betreff:* Re: [gmx-users] File editing - only one layer of water around
>> a molecule
>>
>> On 12/04/2012 3:24 AM, Justin A. Lemkul wrote:
>> >
>> >
>> > Lara Bunte wrote:
>> >> Could you please give how g_select is used?
>>
>> Reading g_select -h might have led you to try g_select -select 'help'
>>
>> >> Is there a tutorial for that?
>> >>
>> >
>> > g_select -select 'help all'
>> >
>> > The information contained therein is very extensive, so be sure to read
>> it thoroughly.  It will fill several terminal windows explaining the syntax
>> and providing examples.
>>
>> ... and search Google for some examples.
>>
>> 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
>>
>>
>>
>> --
>> 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
>>
>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
>



-- 
Cordiali saluti, Dr.Oteri Francesco
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[gmx-users] Need help with tabulated non-bonding potential tablep file

[Marcelo Lopez]

Hi all: I'm trying to run a coarse grained system with 3 different
kind of particles, lets call them "A", "B" and "C", and the
interactions between them are set by means of 3 tabulated potentials
(not LJ, totally customized ones). I want to introduce 1-4
interactions with the -tablep optional argument of mdrun. I don't
understand:

1) How exactly to write one tablep.xvg file? 3 or 4 values for each
pair? For example, for the atom indexes 1 and 5, must I write

1   5   0.0   0.0
or
1    5    0.0
?

Or must I write the atom labels?:

AB0.0   0.0

2) Must I put only one tablep.xvg file with all the pairs or must I
make one separated table for each kind of 1-4 interaction? For
example:

tablep.xvg (with all the interactions)

or

tablep.xvg, tablep_A_A.xvg, tablep_B_B.xvg, tablep_A_C.xvg, ..

3) mdrun expects the indexes and 1 or 2 values?

4) What's the meaning of the value/s at the right of the 2 indexes for
a not LJ tabulated potential?

5) The pair interactions are scaled or set to zero when using
tabulated non-bonding potentials? I need to set them zero...

Thank you in advance.

Johny.
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Re: [gmx-users] File editing - only one layer of water around a molecule

[francesco oteri]

Hi Lara,
the simplest way is using vmd.
Briefly,
1) load the pdb file in vmd.
2) create a representation using a string like:  "same residue as within 3.
of protein".
where "protein" is the group around the molecule you have to use, I
used protein just as example




Il giorno 13 aprile 2012 11:29, Lara Bunte  ha scritto:

> I read g_select -select 'help all' and I understand nothing of that.
>
> In general one have a molecule (valences closed by hydrogen) and a water
> box around it. How to select only the protein with the first water layers,
> say one layer?
>
> Please give me an example how to do this with gromacs. I read the examples
> in g_select -select 'help all' and I have no Idea what they are talking
> about.
>
> Thanks for help
> Greetings
> Lara
>
>
>
>   --
> *Von:* Mark Abraham 
> *An:* Discussion list for GROMACS users 
> *Gesendet:* 19:26 Mittwoch, 11.April 2012
>
> *Betreff:* Re: [gmx-users] File editing - only one layer of water around
> a molecule
>
> On 12/04/2012 3:24 AM, Justin A. Lemkul wrote:
> >
> >
> > Lara Bunte wrote:
> >> Could you please give how g_select is used?
>
> Reading g_select -h might have led you to try g_select -select 'help'
>
> >> Is there a tutorial for that?
> >>
> >
> > g_select -select 'help all'
> >
> > The information contained therein is very extensive, so be sure to read
> it thoroughly.  It will fill several terminal windows explaining the syntax
> and providing examples.
>
> ... and search Google for some examples.
>
> 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
>
>
>
> --
> 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
>



-- 
Cordiali saluti, Dr.Oteri Francesco
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Re: [gmx-users] File editing - only one layer of water around a molecule

[Lara Bunte]

I read g_select -select 'help all' and I understand nothing of that. 


In general one have a molecule (valences closed by hydrogen) and a water box 
around it. How to select only the protein with the first water layers, say one 
layer? 

Please give me an example how to do this with gromacs. I read the examples in 
g_select -select 'help all' and I have no Idea what they are talking about. 


Thanks for help
Greetings
Lara






 Von: Mark Abraham 
An: Discussion list for GROMACS users  
Gesendet: 19:26 Mittwoch, 11.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a 
molecule
 
On 12/04/2012 3:24 AM, Justin A. Lemkul wrote:
> 
> 
> Lara Bunte wrote:
>> Could you please give how g_select is used?

Reading g_select -h might have led you to try g_select -select 'help'

>> Is there a tutorial for that?
>> 
> 
> g_select -select 'help all'
> 
> The information contained therein is very extensive, so be sure to read it 
> thoroughly.  It will fill several terminal windows explaining the syntax and 
> providing examples.

... and search Google for some examples.

Mark
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[gmx-users] Simulation of the pure lipid bilayer

[James Starlight]

Dear Gromacs Users!


I want to perform simulation of the pure bilayer surrounded by water. I'm
using already pre-equilibrated bilayers as the initial structure. During
conversion pdb-> gro -> pdb the velocities from initial equilibration runs
of the structure were lost. Should I start generating this velocities in my
production run ( gen_Vel= yes) or i must do equilibration instead first to
generate velocities? Finally what length should this equilibration be to
provide reasonable velocities for futrher MD run if I would avoild long
equilibration period because of suitability of my initial model?


Thanks for help,


James
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