Re: [gmx-users] Steered Molecular Dynamics (SMD) in Gromcas-4.0.5

[Carsten Kutzner]

Hi,

you should set one pull group, not 700. The number of atoms in your
pull group is 700. Freezing the pull group in x and y direction probably
does what you want. Please also consider to upgrade to 4.0.7,
which is the most recent stable version.

Best,
  Carsten


On Jan 22, 2010, at 7:41 AM, toby10222...@sina.com wrote:

> Dear all:
>I’m using Gromacs-4.0.5 and I want to use the pull code to pull a slab 
> of griphene to move along the Z direction in the simulation (Steered 
> Molecular Dynamics-SMD). The griphene has 700 carbon atoms and the positions 
> of the 700 atoms are expected to be immobile in the X and Y direction.
> The following is the PULL CODE in my mdp file. However, when I used this code 
> for my simulation the error always came out as “Number of weights (1) for 
> pull group 1 'sla' does not match the number of atoms (700)”.
> So here are my doubts about this simulation:
> 1.   Can Gromacs-4.0.5 do this for me, especially keeping the C atoms 
> immobile in X and Y direction while moving along the Z direction?
> 2.   In my simulation, every carbon atom in the slab of griphene was 
> defined as a group. Is it right?
> 3.   How to give the “pull_weights1” to avoid the above ERROR?
> Any suggestions and answers are welcome. Thank you in advance!
>  
> ; COM PULLING  
> ; Pull type: no, umbrella, constraint or constant_force
> pull = constant_force
> ; Pull geometry: distance, direction, cylinder or position
> pull_geometry= distance
> ; Select components for the pull vector. default: Y Y Y
> pull_dim = N N Y
> ; Cylinder radius for dynamic reaction force groups (nm)
> pull_r1  = 
> ; Switch from r1 to r0 in case of dynamic reaction force
> pull_r0  = 
> pull_constr_tol  = 1e-06
> pull_start   = no
> pull_nstxout = 10
> pull_nstfout = 10
> ; Number of pull groups 
> pull_ngroups = 700
> ; Group name, weight (default all 1), vector, init, rate (nm/ps), 
> kJ/(mol*nm^2)
> pull_group0  = 
> pull_weights0= 
> pull_pbcatom0= 
> pull_group1  = sla
> pull_weights1= 1
> pull_pbcatom1= 0
> pull_vec1= 0.0 0.0 1.0
> pull_init1   = 0.0
> pull_rate1   = 0
> pull_k1  = 1.2e-4
> pull_kB1 = 0
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RE: [gmx-users] electrostatic forces

[Berk Hess]

Hi,

I guess this is caused by the 1-4 interactions.
These also contain electrostatic interactions, which are turned off when
you turn off the charges, but not by the energygrp_excl option.

Berk

From: gianfranco.bocchinf...@uniroma2.it
To: gmx-users@gromacs.org
Date: Thu, 21 Jan 2010 18:58:14 +0100
Subject: [gmx-users] electrostatic forces
















Hi,

 

I would like to calculate the electrostatic
forces on the atoms of an Indole group (in a TRP residue). 

I have performed two reruns of my
simulation with two different topologies : a normal topology and a topology
with all the Indole charges set equal to 0.  I have also added
energygrp_excl = Indole Indole (to delete electrostatic force inside the
Indole) and also I have deleted in both topologies all the pairs between atoms
belonging to the Indole group (to delete the electrostatic contribution coming
from 1-4 interactions inside the Indole group). Furthermore I have used a very
simple mdp file (with cut-off, without DispCorr etc.) to avoid contribution
coming, for example, from ewald summation. In these conditions I expected that
the differences between the forces computed in the two simulations were due
only to the electrostatic interactions with the other atoms of protein and with
solvent (SPC). 

Checking the obtained forces I see that
atoms of the Indole (i.e. the CD2 and CE2), with charges equal to 0 in both
topologies, show different forces in the two simulations.

What could be the origin of this
difference?  

 

 

Thank you 

Gianfranco

 

  
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Re: [gmx-users] Lipid parameters for GROMOS96 force fields

[XAvier Periole]

Here is another paper related to the secondary structure propensity
of different force field.

Are current Molecular Dynamics FFs too helical? Best et al:  
BiophysJ-2008

doi:10.1529/biophysj.108.132696

Note that these papers do not report the unstability of helices in  
proteins!


On Jan 22, 2010, at 1:03 AM, Krzysztof Mlynarczyk wrote:


Thank you!!!
The evidence presented in this paper is stunning. It also stresses  
the importance of using the electrostatics treatment that was  
originally used for development of a particular force field, e.g.  
reaction field in case of G96 - the popular PME in connection with  
G53a6 results in even stronger beta sheet bias. This way using this  
force field is out of the question, unless until corrections are  
made and tested. I need a different solution for my problem.


Christopher

2010/1/21 Erik Marklund 
It is documented. Have a look at this one:

Dirk Matthes and Bert L. de Groot.  Secondary structure propensities  
in peptide folding simulations: A systematic comparison of molecular  
mechanics interaction schemes.  Biophys. J.  97:599-608 (2009)


Erik

XAvier Periole skrev:


The instability of helices with the G53a6 force field is definitely  
real

and unfortunately not documented. Some people are working on it ...

I would advise to be very carefull in interpreting results with this  
FF.


XAvier.

On Jan 21, 2010, at 2:13 PM, Justin A. Lemkul wrote:



Krzysztof Mlynarczyk wrote:
2010/1/21 Justin A. Lemkul mailto:jalem...@vt.edu>>
  Krzysztof Mlynarczyk wrote:
  2. If not, is there any way to derive the proper parameters for
  the force field of my choice using the lipid parameters from
  Peter Tieleman's website or e.g. the parameters published by
  Andreas Kukol for G53a6?
  I don't see why you need to do such reverse engineering.  The Kukol
  parameters for lipids under 53a6 can be directly combined with a
  G53a6 protein without any issues; I believe that was the purpose of
  the whole new derivation :)
I received a message that G53a6 is beta-sheet biased and alpha  
helices do not perform as well as they should. My protein contains 7  
transmembrane helices, that's why I'm worried.


Is this published somewhere?  That would be important information.   
Perhaps this is the case for model peptides or short fragments, but  
I have certainly done a number of simulations using 53a6 with well- 
folded globular proteins and I do not see any such instability  
(i.e., alpha->beta conversion or unwinding of alpha-helices).  I do  
believe it is possible in certain scenarios, but I don't know that a  
large 7TM protein like yours would suffer adversely.


I know that there are changes between parameter sets both in non- 
bonded and bonded terms and one rtp entry will probably not work  
well when pasted into a different force field from the same family.  
G96 family uses symbols like gd_5 that are substituted by  
appropriate parameters later through the use of preprocessor. While  
it is possible to find that gd_5 is the same as gd_15 in another  
version of G96 and substitute those symbols in topologies, the  
changes in non bonded parameters still can spoil what was working  
well elsewhere. That's why I was also asking for some checked and  
ready-to-use topologies for a particular force field.


Many of the bonded parameters carry over between force fields, but  
certainly new entries were created between 43a2 and 53a6, so yes,  
some re-working would likely be necessary.  There is a lipid 43a2  
parameter set on the User Contribution site, like I said before, I  
just don't know if there is a reference for it.


  As an aside, you are quite right that multiple force fields within
  the same simulation is incorrect.  However, the Berger lipid
  parameters may be an exception to this rule, since they are really a
  hybridized version of OPLS-UA and Gromos87 parameters (some of which
  were modified anyway), so they really don't belong to any one
  particular force field.  The Berger/G87 combination is widely used,
  but essentially amounts to the following: lipid interactions are
  Berger-Berger or OPLS-OPLS interactions, while protein-lipid
  interations are Berger-G87, and protein-protein interactions are
  G87-G87.  You can see quite quickly why things become complicated!
  Based on a discussion I had with Dr. Tieleman, it seems to be
  reasonable to use the G96 parameter set of your choice in
  conjunction with lipid.itp (Berger lipids), although other
  approaches may be more rigorously correct (pure G96 parameters such
  as those by Kukol, pure OPLS recently derived by Ulmschneider, or
  the modifications to the Berger parameters from the Tieleman group,
  to name a few).  If you want to use a G96-lipid.itp combination, I
  created a tutorial that teaches you how to build the system and
  properly prepare the topology.  It is linked from the Tutorials page
  of the Gromacs site.
I found this tutorial earlier and was also in do

R: [gmx-users] electrostatic forces

[Gianfranco Bocchinfuso]

Thank you for your reply,

 

Really, I don’t think that the difference come from the 1-4 interactions. 

I have excluded all the 1-4 interaction involving atoms in the indole group
(deleting them from the pairs list). Furthermore, I have added the indole as
an energygrps, and checking the 1-4 energy terms in this group, they are
correctly 0 both in the simulation with the charges and in the simulation
with charges=0

 

Gianfranco

Da: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Per
conto di Berk Hess
Inviato: venerdì 22 gennaio 2010 9.11
A: Discussion list for GROMACS users
Oggetto: RE: [gmx-users] electrostatic forces

 

Hi,

I guess this is caused by the 1-4 interactions.
These also contain electrostatic interactions, which are turned off when
you turn off the charges, but not by the energygrp_excl option.

Berk

  _  

From: gianfranco.bocchinf...@uniroma2.it
To: gmx-users@gromacs.org
Date: Thu, 21 Jan 2010 18:58:14 +0100
Subject: [gmx-users] electrostatic forces

Hi,

 

I would like to calculate the electrostatic forces on the atoms of an Indole
group (in a TRP residue). 

I have performed two reruns of my simulation with two different topologies :
a normal topology and a topology with all the Indole charges set equal to 0.
I have also added energygrp_excl = Indole Indole (to delete electrostatic
force inside the Indole) and also I have deleted in both topologies all the
pairs between atoms belonging to the Indole group (to delete the
electrostatic contribution coming from 1-4 interactions inside the Indole
group). Furthermore I have used a very simple mdp file (with cut-off,
without DispCorr etc.) to avoid contribution coming, for example, from ewald
summation. In these conditions I expected that the differences between the
forces computed in the two simulations were due only to the electrostatic
interactions with the other atoms of protein and with solvent (SPC). 

Checking the obtained forces I see that atoms of the Indole (i.e. the CD2
and CE2), with charges equal to 0 in both topologies, show different forces
in the two simulations.

What could be the origin of this difference?  

 

 

Thank you 

Gianfranco

 

 

  _  

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[gmx-users] Load imbalance

[Carla Jamous]

Hi everyone,

Lately I've been using gromacs version 3.3.3. Yesterday, I started
simulations in a cluster where gromacs version is 4.0.3.
After a run, I got this error message:
 Average load imbalance: 0.5 %
 Part of the total run time spent waiting due to load imbalance: 0.3 %
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0
% Y 0 %
 Average PME mesh/force load: 0.898
 Part of the total run time spent waiting due to PP/PME imbalance: 2.7 %

I don't have a clue what this means & how can I fix it?

Please can anyone help?

Thank you
Carla
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Re: [gmx-users] Load imbalance

[Erik Marklund]

Carla Jamous skrev:

Hi everyone,

Lately I've been using gromacs version 3.3.3. Yesterday, I started 
simulations in a cluster where gromacs version is 4.0.3.

After a run, I got this error message:
 Average load imbalance: 0.5 %
 Part of the total run time spent waiting due to load imbalance: 0.3 %
 Steps where the load balancing was limited by -rdd, -rcon and/or 
-dds: X 0 % Y 0 %

 Average PME mesh/force load: 0.898
 Part of the total run time spent waiting due to PP/PME imbalance: 2.7 %

I don't have a clue what this means & how can I fix it?

Please can anyone help?

Thank you
Carla
This is no error message. 0.5 % load imbalance just means that the 
workload was distributed in a good way over procesors throughout your 
simulation.


--
---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys

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Re: [gmx-users] Load imbalance

[Justin A. Lemkul]

Carla Jamous wrote:

Hi everyone,

Lately I've been using gromacs version 3.3.3. Yesterday, I started 
simulations in a cluster where gromacs version is 4.0.3.


Why start with 4.0.3?  You should be using the latest stable version (4.0.7).


After a run, I got this error message:
 Average load imbalance: 0.5 %
 Part of the total run time spent waiting due to load imbalance: 0.3 %
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: 
X 0 % Y 0 %

 Average PME mesh/force load: 0.898
 Part of the total run time spent waiting due to PP/PME imbalance: 2.7 %

I don't have a clue what this means & how can I fix it?


There's nothing that needs to be fixed, per se.  "Load imbalance" has to do with 
how well divided the system in terms of PP/PME balance (discussed in the Gromacs 
manual - read about domain decomposition).  The very small percent imbalance you 
got means you probably achieved decent performance given however this PP/PME 
imbalance.  There are many threads in the list archive about how to make things 
faster and what this all means.  The manual should be the first port of call, 
after which you should have a look in the archives.  If you want to try to 
optimize something about your system, we will need a lot more information - the 
DD grid, .mdp file, how many nodes are being assigned for PME (and whether or 
not you're doing it manually), etc.


-Justin



Please can anyone help?

Thank you
Carla



--


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] Load imbalance

[Carla Jamous]

Yes, but I forgot to say that I got this note that followed:
5.4 % performance was lost because the PME nodes
  had less work to do than the PP nodes.
  You might want to decrease the number of PME nodes
  or decrease the cut-off and the grid spacing.

Carla

On Fri, Jan 22, 2010 at 1:34 PM, Erik Marklund  wrote:

> Carla Jamous skrev:
>
>  Hi everyone,
>>
>> Lately I've been using gromacs version 3.3.3. Yesterday, I started
>> simulations in a cluster where gromacs version is 4.0.3.
>> After a run, I got this error message:
>>  Average load imbalance: 0.5 %
>>  Part of the total run time spent waiting due to load imbalance: 0.3 %
>>  Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X
>> 0 % Y 0 %
>>  Average PME mesh/force load: 0.898
>>  Part of the total run time spent waiting due to PP/PME imbalance: 2.7 %
>>
>> I don't have a clue what this means & how can I fix it?
>>
>> Please can anyone help?
>>
>> Thank you
>> Carla
>>
> This is no error message. 0.5 % load imbalance just means that the workload
> was distributed in a good way over procesors throughout your simulation.
>
> --
> ---
> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 4537fax: +46 18 511 755
> er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys
>
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Re: [gmx-users] Load imbalance

[Justin A. Lemkul]

Carla Jamous wrote:

Yes, but I forgot to say that I got this note that followed:
5.4 % performance was lost because the PME nodes
  had less work to do than the PP nodes.
  You might want to decrease the number of PME nodes
  or decrease the cut-off and the grid spacing.



5% loss still isn't that bad.  I've achieved good results with worse loss :)  It 
all depends (again) on your setup.  When you built the .tpr file, grompp should 
have reported what it predicted for the % of the load that PME should be 
calculating.  For most cases, it will be best if it is 25-33%, such that the 
PP/PME ratio can be 3:1 or 2:1.  If you don't achieve absolute perfection (which 
is rare), you're going to experience some small performance loss.  You can (as 
the message is indicating to you) tweak some of the input parameters, such as 
the Fourier grid spacing, to try to re-balance things.


Again, much of this is in the manual and the Gromacs 4 paper.

-Justin


Carla

On Fri, Jan 22, 2010 at 1:34 PM, Erik Marklund > wrote:


Carla Jamous skrev:

Hi everyone,

Lately I've been using gromacs version 3.3.3. Yesterday, I
started simulations in a cluster where gromacs version is 4.0.3.
After a run, I got this error message:
 Average load imbalance: 0.5 %
 Part of the total run time spent waiting due to load imbalance:
0.3 %
 Steps where the load balancing was limited by -rdd, -rcon
and/or -dds: X 0 % Y 0 %
 Average PME mesh/force load: 0.898
 Part of the total run time spent waiting due to PP/PME
imbalance: 2.7 %

I don't have a clue what this means & how can I fix it?

Please can anyone help?

Thank you
Carla

This is no error message. 0.5 % load imbalance just means that the
workload was distributed in a good way over procesors throughout
your simulation.

-- 
---

Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.se   
 http://xray.bmc.uu.se/molbiophys


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--


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] Load imbalance

[Erik Marklund]

Well, there you go. That message tells you how to improve performance. 
Changing the number of PME-nodes to improve performance may or may not 
be doable, depending on the number of processors availvable. On the 
other hand, 5.4 % performance loss is not that bad in my oppinion.


There is a tool fopr tuning the number of PME-nodes that you could try: 
g_tune_pme. I've never used it myself though, so I don't know what to 
expect form it.


/Erik

Carla Jamous skrev:

Yes, but I forgot to say that I got this note that followed:
5.4 % performance was lost because the PME nodes
  had less work to do than the PP nodes.
  You might want to decrease the number of PME nodes
  or decrease the cut-off and the grid spacing.

Carla

On Fri, Jan 22, 2010 at 1:34 PM, Erik Marklund > wrote:


Carla Jamous skrev:

Hi everyone,

Lately I've been using gromacs version 3.3.3. Yesterday, I
started simulations in a cluster where gromacs version is 4.0.3.
After a run, I got this error message:
 Average load imbalance: 0.5 %
 Part of the total run time spent waiting due to load
imbalance: 0.3 %
 Steps where the load balancing was limited by -rdd, -rcon
and/or -dds: X 0 % Y 0 %
 Average PME mesh/force load: 0.898
 Part of the total run time spent waiting due to PP/PME
imbalance: 2.7 %

I don't have a clue what this means & how can I fix it?

Please can anyone help?

Thank you
Carla

This is no error message. 0.5 % load imbalance just means that the
workload was distributed in a good way over procesors throughout
your simulation.

-- 
---

Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.se   
 http://xray.bmc.uu.se/molbiophys


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--
---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys

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[gmx-users] [ dummies 2] or [ virtual_sites 2] not works.

[yoochan,myung]

Hi.

I'm on QM/MM simulation (gromacs-gaussian03).

I exactly followed under reference, but I could't success. 
http://wwwuser.gwdg.de/~ggroenh/EMBO2004/html/qmmmvacuum.html#top



 I checked presence of two LA atoms in [ atoms] of TOP file.

Also, I checked under [ dummies 2] and [ constraints ]in Top file.
(I think, [ dummies 2] = [ virtual_sites 2] but,  [ virtual_sites 2] in 4.x.x 
Gromacs, [ dummies 2] in  3.x.x)

[ dummies 2]
1279 906 904 1 0.72
1280 938 936 1 0.72

[ constraints ]
906 904 2 0.153
938 936 2 0.153


And then, I did GROMPP, I got this error message.
(In reference, there is a "run.scr " step which is multiple GROMPP and MDRUN  
running scripts.)

'Atom type "LA" not found'


I think grompp doesn't recognize atom "LA" on [ atoms ] as dummies.

Any suggestions?


Regards.

yoochan,--
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[gmx-users] cut-off

[nishap . patel]

Hello,

I wanted to know, if say my box is 30A (cubic) and if I set my  
cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that mean,  
the simulation will cut-0ff at 9A? Should I be changing that to 1.5nm  
(to get half the box cut-off)? I am a little confused about that.


Thanks.

Nisha Patel


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Re: [gmx-users] cut-off

[Justin A. Lemkul]

nishap.pa...@utoronto.ca wrote:

Hello,

I wanted to know, if say my box is 30A (cubic) and if I set my 
cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that mean, 
the simulation will cut-0ff at 9A? Should I be changing that to 1.5nm 
(to get half the box cut-off)? I am a little confused about that.




Setting rvdw = 0.9 means that van der Waals interactions beyond 0.9 nm are zero. 
  It has no effect on, for example, Coulombic interactions.


Most force fields have defined cutoffs that should be used in order to be 
consistent with the original derivation of the parameter set, so it is generally 
inadvisable to make ad hoc changes to the cutoffs in order to meet some 
arbitrary criterion.  The minimum image convention specifies that your longest 
cutoff must always be less than half the smallest box vector.  If you set up a 
system with a cutoff equal to exactly one half of a box vector, if that box 
vector decreases even slightly (i.e., under the influence of pressure coupling), 
then you will be calculating spurious forces.


-Justin


Thanks.

Nisha Patel




--


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] cut-off

[nishap . patel]

I see what you mean, so say if I am doing RDF, the values beyond 9A  
would be bogus?



Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:

Hello,

   I wanted to know, if say my box is 30A (cubic) and if I set my   
cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that   
mean, the simulation will cut-0ff at 9A? Should I be changing that   
to 1.5nm (to get half the box cut-off)? I am a little confused   
about that.




Setting rvdw = 0.9 means that van der Waals interactions beyond 0.9 nm
are zero.   It has no effect on, for example, Coulombic interactions.

Most force fields have defined cutoffs that should be used in order to
be consistent with the original derivation of the parameter set, so it
is generally inadvisable to make ad hoc changes to the cutoffs in order
to meet some arbitrary criterion.  The minimum image convention
specifies that your longest cutoff must always be less than half the
smallest box vector.  If you set up a system with a cutoff equal to
exactly one half of a box vector, if that box vector decreases even
slightly (i.e., under the influence of pressure coupling), then you
will be calculating spurious forces.

-Justin


Thanks.

Nisha Patel




--


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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Nisha Patel
MSc Candidate
Leslie Dan Faculty of Pharmacy
Department of Pharmaceutical Sciences
144 College Street
Room 1172
Toronto, ON
M5S 3M2
Canada
Telephone: 416-978-1536

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Re: [gmx-users] cut-off

[Justin A. Lemkul]

nishap.pa...@utoronto.ca wrote:
I see what you mean, so say if I am doing RDF, the values beyond 9A 
would be bogus?




To a large extent, probably, but I don't think that I can say that absolutely 
without context.  For example, you've only shown us rvdw, what about rcoulomb? 
If it is longer for some reason, then this value will also influence the RDF. 
Long-range electrostatics (i.e., PME) may have some effect as well, but I don't 
really have much detailed experience in doing that sort of thing.


There is a nice section in the manual about RDF calculation, as well as an 
example RDF plot for SPC water that should give you an idea of what to expect, 
in general.


-Justin



Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:

Hello,

   I wanted to know, if say my box is 30A (cubic) and if I set my  
cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that  
mean, the simulation will cut-0ff at 9A? Should I be changing that  
to 1.5nm (to get half the box cut-off)? I am a little confused  about 
that.




Setting rvdw = 0.9 means that van der Waals interactions beyond 0.9 nm
are zero.   It has no effect on, for example, Coulombic interactions.

Most force fields have defined cutoffs that should be used in order to
be consistent with the original derivation of the parameter set, so it
is generally inadvisable to make ad hoc changes to the cutoffs in order
to meet some arbitrary criterion.  The minimum image convention
specifies that your longest cutoff must always be less than half the
smallest box vector.  If you set up a system with a cutoff equal to
exactly one half of a box vector, if that box vector decreases even
slightly (i.e., under the influence of pressure coupling), then you
will be calculating spurious forces.

-Justin


Thanks.

Nisha Patel




--


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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Nisha Patel
MSc Candidate
Leslie Dan Faculty of Pharmacy
Department of Pharmaceutical Sciences
144 College Street
Room 1172
Toronto, ON
M5S 3M2
Canada
Telephone: 416-978-1536



--


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] question

[akram gorji]

Hi,I want to simulate a finite nono-tubes.Does nonotube be flexible or
rigid?which is better?thanks
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Re: [gmx-users] question

[David van der Spoel]

On 1/22/10 9:11 PM, akram gorji wrote:

Hi,I want to simulate a finite nono-tubes.Does nonotube be flexible or
rigid?which is better?thanks


Do you mean nano tubes?

Try some literature search. Quite a bit has been done on this topic, 
also with GROMACS.


--
David.

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se

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[gmx-users] diketopiperazine

[Jose Tusell]

Hi,

I'm trying to construct diketopiperazine with gromacs.  The problem that I
have right now is forming the bond that unites the C and N termi to make the
cyclic peptide.  I tried using specbond.dat but so far I've been
unsucessful.  Here is my specbond.dat file and pdb file:

specbond.dat
8
CYS SG  1   CYS SG  1   0.2 CYS2CYS2
CYS SG  1   HEMEFE  2   0.25CYS2HEME
CYS SG  1   HEMECAB 1   0.18CYS2HEME
CYS SG  1   HEMECAC 1   0.18CYS2HEME
HIS NE2 1   HEMEFE  1   0.2 HIS1HEME
MET SD  1   HEMEFE  1   0.24MET HEME
CYM SG  1   CYM SG  1   0.2 CYS2CYS2
TRP  N  1   HISH C  1   0.2 TRP HISH

whdikp.pdb
REMARK   S  14 x 14 mn oif
ATOM  1  N   TRP1   -0.813   0.594   1.164
ATOM  2  H   TRP1   -0.249   1.064   1.843
ATOM  3  CA  TRP1   -0.264  -0.210   0.004
ATOM  4  HA  TRP10.855  -0.244   0.066
ATOM  5  CB  TRP1   -0.633   0.484  -1.321
ATOM  6  HB1 TRP1   -1.672   0.344  -1.531
ATOM  7  HB2 TRP1   -0.408   1.528  -1.262
ATOM  8  CG  TRP10.205  -0.166  -2.397
ATOM  9  CD1 TRP10.227  -1.464  -2.727
ATOM 10  HD1 TRP1   -0.407  -2.173  -2.195
ATOM 11  CD2 TRP11.119   0.455  -3.258
ATOM 12  NE1 TRP11.166  -1.607  -3.796
ATOM 13  HE1 TRP11.401  -2.473  -4.259
ATOM 14  CE2 TRP11.673  -0.432  -4.078
ATOM 15  CE3 TRP11.485   1.803  -3.344
ATOM 16  HE3 TRP11.065   2.575  -2.699
ATOM 17  CZ2 TRP12.626  -0.117  -5.054
ATOM 18  HZ2 TRP13.035  -0.902  -5.690
ATOM 19  CZ3 TRP12.444   2.145  -4.320
ATOM 20  HZ3 TRP12.741   3.190  -4.402
ATOM 21  CH2 TRP12.990   1.222  -5.140
ATOM 22  HH2 TRP13.727   1.540  -5.878
ATOM 23  C   TRP1   -0.816  -1.621   0.004
ATOM 24  O   TRP1   -0.072  -2.712   0.004
ATOM 25  N   HISH   2   -2.331  -1.621   0.004
ATOM 26  H   HISH   2   -2.895  -2.093  -0.674
ATOM 27  CA  HISH   2   -2.881  -0.816   1.162
ATOM 28  HA  HISH   2   -4.000  -0.781   1.098
ATOM 29  CB  HISH   2   -2.516  -1.510   2.488
ATOM 30  HB1 HISH   2   -1.564  -1.990   2.400
ATOM 31  HB2 HISH   2   -2.494  -0.794   3.283
ATOM 32  CG  HISH   2   -3.591  -2.538   2.747
ATOM 33  ND1 HISH   2   -3.867  -3.560   1.846
ATOM 34  HD1 HISH   2   -3.399  -3.715   0.964
ATOM 35  CD2 HISH   2   -4.447  -2.700   3.792
ATOM 36  HD2 HISH   2   -4.608  -2.157   4.723
ATOM 37  CE1 HISH   2   -4.846  -4.291   2.344
ATOM 38  HE1 HISH   2   -5.219  -5.152   1.791
ATOM 39  NE2 HISH   2   -5.203  -3.793   3.502
ATOM 40  HE2 HISH   2   -5.932  -4.166   4.093
ATOM 41  C   HISH   2   -2.329   0.595   1.164
ATOM 42  O   HISH   2   -3.089   1.710   1.164

Thanks for any suggestions,

Jose Tusell
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Re: [gmx-users] diketopiperazine

[Justin A. Lemkul]

Jose Tusell wrote:

Hi,

I'm trying to construct diketopiperazine with gromacs.  The problem that 
I have right now is forming the bond that unites the C and N termi to 
make the cyclic peptide.  I tried using specbond.dat but so far I've 
been unsucessful.  Here is my specbond.dat file and pdb file:




I believe there is a fundamental limitation with pdb2gmx - it doesn't deal with 
cyclic species.  Every post I've seen about this issue has been along the lines 
of "generate the normal topology and add the missing bonded parameters manually."


I also think the specbond.dat file could never work anyway.  The distance 
between your C and N atoms appears to be right about 0.15 nm, so a 0.2-nm 
criterion (+/- 10%) will never detect that a bond should be created between 
these two atoms anyway.  Just FYI for the future.


-Justin


specbond.dat
8
CYS SG  1   CYS SG  1   0.2 CYS2CYS2
CYS SG  1   HEMEFE  2   0.25CYS2HEME
CYS SG  1   HEMECAB 1   0.18CYS2HEME
CYS SG  1   HEMECAC 1   0.18CYS2HEME
HIS NE2 1   HEMEFE  1   0.2 HIS1HEME
MET SD  1   HEMEFE  1   0.24MET HEME
CYM SG  1   CYM SG  1   0.2 CYS2CYS2
TRP  N  1   HISH C  1   0.2 TRP HISH

whdikp.pdb
REMARK   S  14 x 14 mn oif
ATOM  1  N   TRP1   -0.813   0.594   1.164
ATOM  2  H   TRP1   -0.249   1.064   1.843
ATOM  3  CA  TRP1   -0.264  -0.210   0.004
ATOM  4  HA  TRP10.855  -0.244   0.066
ATOM  5  CB  TRP1   -0.633   0.484  -1.321
ATOM  6  HB1 TRP1   -1.672   0.344  -1.531
ATOM  7  HB2 TRP1   -0.408   1.528  -1.262
ATOM  8  CG  TRP10.205  -0.166  -2.397
ATOM  9  CD1 TRP10.227  -1.464  -2.727
ATOM 10  HD1 TRP1   -0.407  -2.173  -2.195
ATOM 11  CD2 TRP11.119   0.455  -3.258
ATOM 12  NE1 TRP11.166  -1.607  -3.796
ATOM 13  HE1 TRP11.401  -2.473  -4.259
ATOM 14  CE2 TRP11.673  -0.432  -4.078
ATOM 15  CE3 TRP11.485   1.803  -3.344
ATOM 16  HE3 TRP11.065   2.575  -2.699
ATOM 17  CZ2 TRP12.626  -0.117  -5.054
ATOM 18  HZ2 TRP13.035  -0.902  -5.690
ATOM 19  CZ3 TRP12.444   2.145  -4.320
ATOM 20  HZ3 TRP12.741   3.190  -4.402
ATOM 21  CH2 TRP12.990   1.222  -5.140
ATOM 22  HH2 TRP13.727   1.540  -5.878
ATOM 23  C   TRP1   -0.816  -1.621   0.004
ATOM 24  O   TRP1   -0.072  -2.712   0.004
ATOM 25  N   HISH   2   -2.331  -1.621   0.004
ATOM 26  H   HISH   2   -2.895  -2.093  -0.674
ATOM 27  CA  HISH   2   -2.881  -0.816   1.162
ATOM 28  HA  HISH   2   -4.000  -0.781   1.098
ATOM 29  CB  HISH   2   -2.516  -1.510   2.488
ATOM 30  HB1 HISH   2   -1.564  -1.990   2.400
ATOM 31  HB2 HISH   2   -2.494  -0.794   3.283
ATOM 32  CG  HISH   2   -3.591  -2.538   2.747
ATOM 33  ND1 HISH   2   -3.867  -3.560   1.846
ATOM 34  HD1 HISH   2   -3.399  -3.715   0.964
ATOM 35  CD2 HISH   2   -4.447  -2.700   3.792
ATOM 36  HD2 HISH   2   -4.608  -2.157   4.723
ATOM 37  CE1 HISH   2   -4.846  -4.291   2.344
ATOM 38  HE1 HISH   2   -5.219  -5.152   1.791
ATOM 39  NE2 HISH   2   -5.203  -3.793   3.502
ATOM 40  HE2 HISH   2   -5.932  -4.166   4.093
ATOM 41  C   HISH   2   -2.329   0.595   1.164
ATOM 42  O   HISH   2   -3.089   1.710   1.164

Thanks for any suggestions,

Jose Tusell



--


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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Subject: [gmx-users] [ dummies 2] or [ virtual_sites 2] not works.

[Gerrit Groenhof]

> CYM SG  1   CYM SG  1   0.2 CYS2CYS2
> TRP  N  1   HISH C  1   0.2 TRP HISH
> 
> whdikp.pdb
> REMARK   S  14 x 14 mn oif
> ATOM  1  N   TRP1   -0.813   0.594   1.164
> ATOM  2  H   TRP1   -0.249   1.064   1.843
> ATOM  3  CA  TRP1   -0.264  -0.210   0.004
> ATOM  4  HA  TRP10.855  -0.244   0.066
> ATOM  5  CB  TRP1   -0.633   0.484  -1.321
> ATOM  6  HB1 TRP1   -1.672   0.344  -1.531
> ATOM  7  HB2 TRP1   -0.408   1.528  -1.262
> ATOM  8  CG  TRP10.205  -0.166  -2.397
> ATOM  9  CD1 TRP10.227  -1.464  -2.727
> ATOM 10  HD1 TRP1   -0.407  -2.173  -2.195
> ATOM 11  CD2 TRP11.119   0.455  -3.258
> ATOM 12  NE1 TRP11.166  -1.607  -3.796
> ATOM 13  HE1 TRP11.401  -2.473  -4.259
> ATOM 14  CE2 TRP11.673  -0.432  -4.078
> ATOM 15  CE3 TRP11.485   1.803  -3.344
> ATOM 16  HE3 TRP11.065   2.575  -2.699
> ATOM 17  CZ2 TRP12.626  -0.117  -5.054
> ATOM 18  HZ2 TRP13.035  -0.902  -5.690
> ATOM 19  CZ3 TRP12.444   2.145  -4.320
> ATOM 20  HZ3 TRP12.741   3.190  -4.402
> ATOM 21  CH2 TRP12.990   1.222  -5.140
> ATOM 22  HH2 TRP13.727   1.540  -5.878
> ATOM 23  C   TRP1   -0.816  -1.621   0.004
> ATOM 24  O   TRP1   -0.072  -2.712   0.004
> ATOM 25  N   HISH   2   -2.331  -1.621   0.004
> ATOM 26  H   HISH   2   -2.895  -2.093  -0.674
> ATOM 27  CA  HISH   2   -2.881  -0.816   1.162
> ATOM 28  HA  HISH   2   -4.000  -0.781   1.098
> ATOM 29  CB  HISH   2   -2.516  -1.510   2.488
> ATOM 30  HB1 HISH   2   -1.564  -1.990   2.400
> ATOM 31  HB2 HISH   2   -2.494  -0.794   3.283
> ATOM 32  CG  HISH   2   -3.591  -2.538   2.747
> ATOM 33  ND1 HISH   2   -3.867  -3.560   1.846
> ATOM 34  HD1 HISH   2   -3.399  -3.715   0.964
> ATOM 35  CD2 HISH   2   -4.447  -2.700   3.792
> ATOM 36  HD2 HISH   2   -4.608  -2.157   4.723
> ATOM 37  CE1 HISH   2   -4.846  -4.291   2.344
> ATOM 38  HE1 HISH   2   -5.219  -5.152   1.791
> ATOM 39  NE2 HISH   2   -5.203  -3.793   3.502
> ATOM 40  HE2 HISH   2   -5.932  -4.166   4.093
> ATOM 41  C   HISH   2   -2.329   0.595   1.164
> ATOM 42  O   HISH   2   -3.089   1.710   1.164
> 
> Thanks for any suggestions,
> 
> Jose Tusell
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Re: [gmx-users] diketopiperazine

[Jose Tusell]

Thanks Justin, I used specbond.dat with a 0.15nm searching distance to
create the bond, it seemed to work.

Ramon

On Fri, Jan 22, 2010 at 2:40 PM, Justin A. Lemkul  wrote:

>
>
> Jose Tusell wrote:
>
>> Hi,
>>
>> I'm trying to construct diketopiperazine with gromacs.  The problem that I
>> have right now is forming the bond that unites the C and N termi to make the
>> cyclic peptide.  I tried using specbond.dat but so far I've been
>> unsucessful.  Here is my specbond.dat file and pdb file:
>>
>>
> I believe there is a fundamental limitation with pdb2gmx - it doesn't deal
> with cyclic species.  Every post I've seen about this issue has been along
> the lines of "generate the normal topology and add the missing bonded
> parameters manually."
>
> I also think the specbond.dat file could never work anyway.  The distance
> between your C and N atoms appears to be right about 0.15 nm, so a 0.2-nm
> criterion (+/- 10%) will never detect that a bond should be created between
> these two atoms anyway.  Just FYI for the future.
>
> -Justin
>
>
>  specbond.dat
>> 8
>> CYS SG  1   CYS SG  1   0.2 CYS2CYS2
>> CYS SG  1   HEMEFE  2   0.25CYS2HEME
>> CYS SG  1   HEMECAB 1   0.18CYS2HEME
>> CYS SG  1   HEMECAC 1   0.18CYS2HEME
>> HIS NE2 1   HEMEFE  1   0.2 HIS1HEME
>> MET SD  1   HEMEFE  1   0.24MET HEME
>> CYM SG  1   CYM SG  1   0.2 CYS2CYS2
>> TRP  N  1   HISH C  1   0.2 TRP HISH
>>
>> whdikp.pdb
>> REMARK   S  14 x 14 mn oif
>> ATOM  1  N   TRP1   -0.813   0.594   1.164
>> ATOM  2  H   TRP1   -0.249   1.064   1.843
>> ATOM  3  CA  TRP1   -0.264  -0.210   0.004
>> ATOM  4  HA  TRP10.855  -0.244   0.066
>> ATOM  5  CB  TRP1   -0.633   0.484  -1.321
>> ATOM  6  HB1 TRP1   -1.672   0.344  -1.531
>> ATOM  7  HB2 TRP1   -0.408   1.528  -1.262
>> ATOM  8  CG  TRP10.205  -0.166  -2.397
>> ATOM  9  CD1 TRP10.227  -1.464  -2.727
>> ATOM 10  HD1 TRP1   -0.407  -2.173  -2.195
>> ATOM 11  CD2 TRP11.119   0.455  -3.258
>> ATOM 12  NE1 TRP11.166  -1.607  -3.796
>> ATOM 13  HE1 TRP11.401  -2.473  -4.259
>> ATOM 14  CE2 TRP11.673  -0.432  -4.078
>> ATOM 15  CE3 TRP11.485   1.803  -3.344
>> ATOM 16  HE3 TRP11.065   2.575  -2.699
>> ATOM 17  CZ2 TRP12.626  -0.117  -5.054
>> ATOM 18  HZ2 TRP13.035  -0.902  -5.690
>> ATOM 19  CZ3 TRP12.444   2.145  -4.320
>> ATOM 20  HZ3 TRP12.741   3.190  -4.402
>> ATOM 21  CH2 TRP12.990   1.222  -5.140
>> ATOM 22  HH2 TRP13.727   1.540  -5.878
>> ATOM 23  C   TRP1   -0.816  -1.621   0.004
>> ATOM 24  O   TRP1   -0.072  -2.712   0.004
>> ATOM 25  N   HISH   2   -2.331  -1.621   0.004
>> ATOM 26  H   HISH   2   -2.895  -2.093  -0.674
>> ATOM 27  CA  HISH   2   -2.881  -0.816   1.162
>> ATOM 28  HA  HISH   2   -4.000  -0.781   1.098
>> ATOM 29  CB  HISH   2   -2.516  -1.510   2.488
>> ATOM 30  HB1 HISH   2   -1.564  -1.990   2.400
>> ATOM 31  HB2 HISH   2   -2.494  -0.794   3.283
>> ATOM 32  CG  HISH   2   -3.591  -2.538   2.747
>> ATOM 33  ND1 HISH   2   -3.867  -3.560   1.846
>> ATOM 34  HD1 HISH   2   -3.399  -3.715   0.964
>> ATOM 35  CD2 HISH   2   -4.447  -2.700   3.792
>> ATOM 36  HD2 HISH   2   -4.608  -2.157   4.723
>> ATOM 37  CE1 HISH   2   -4.846  -4.291   2.344
>> ATOM 38  HE1 HISH   2   -5.219  -5.152   1.791
>> ATOM 39  NE2 HISH   2   -5.203  -3.793   3.502
>> ATOM 40  HE2 HISH   2   -5.932  -4.166   4.093
>> ATOM 41  C   HISH   2   -2.329   0.595   1.164
>> ATOM 42  O   HISH   2   -3.089   1.710   1.164
>>
>> Thanks for any suggestions,
>>
>> Jose Tusell
>>
>>
> --
> 
>
> 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] OPLS force field

[Yanmei Song]

Dear Users:

I build up my polymer molecules in PRODRG and got the .gro and .itp file.
Then anyone knows how I can transfer or edit the itp file into OPLS force
field format?  Or anyone knows how can I get the OPLS force field parameters
if I have my molecule gro file.  Any suggestion will be great thankful.

-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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Re: [gmx-users] OPLS force field

[Justin A. Lemkul]

Yanmei Song wrote:

Dear Users:

I build up my polymer molecules in PRODRG and got the .gro and .itp 
file. Then anyone knows how I can transfer or edit the itp file into 
OPLS force field format?  Or anyone knows how can I get the OPLS force 
field parameters if I have my molecule gro file.  Any suggestion will be 
great thankful.




PRODRG is only suitable for use with Gromos96 force fields.  If you want to 
re-write it for OPLS, you're better off starting from scratch, since you'll have 
to change just about all of it, anyway.


There are several scripts in the User Contribution section of the Gromacs that 
can generate OPLS force fields.  You can also try x2top, but you will likely 
have to come up with .n2t entries to suit whatever your molecule is.


-Justin


--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University



--


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: Steered Molecular Dynamics (SMD) in Gromcas-4.0.5(toby10222...@sina.com)

[toby10222224]

Hi Carsten:
Thank you for your answers. I don't know whether I am right to reply to 
gmx-us...@gromacs.org. If I am wrong, please tell me.
As in my last letter, I said I was not able to set "pull_weights1" correctly. I 
have red the mannual, but I don't understand what it tells. I'll do with your 
recommendation, setting one pull group which contains 700 atoms and using 
Gromacs-4.0.7. Then how to set the "pull_weights1" ?
Best regards!
 
 
Hi,

you should set one pull group, not 700. The number of atoms in your
pull group is 700. Freezing the pull group in x and y direction probably
does what you want. Please also consider to upgrade to 4.0.7,
which is the most recent stable version.

Best,
  Carsten


On Jan 22, 2010, at 7:41 AM, toby10222...@sina.com wrote:

> Dear all:
>I’m using Gromacs-4.0.5 and I want to use the pull code to pull a slab of griphene to move along the Z direction in the simulation (Steered Molecular Dynamics-SMD). The griphene has 700 carbon atoms and the positions of the 700 atoms are expected to be immobile in the X and Y direction.
> The following is the PULL CODE in my mdp file. However, when I used this code for my simulation the error always came out as “Number of weights (1) for pull group 1 'sla' does not match the number of atoms (700)”.
> So here are my doubts about this simulation:
> 1.   Can Gromacs-4.0.5 do this for me, especially keeping the C atoms immobile in X and Y direction while moving along the Z direction?
> 2.   In my simulation, every carbon atom in the slab of griphene was defined as a group. Is it right?
> 3.   How to give the “pull_weights1” to avoid the above ERROR?
> Any suggestions and answers are welcome. Thank you in advance!
>  
> ; COM PULLING  
> ; Pull type: no, umbrella, constraint or constant_force
> pull = constant_force
> ; Pull geometry: distance, direction, cylinder or position
> pull_geometry= distance
> ; Select components for the pull vector. default: Y Y Y
> pull_dim = N N Y
> ; Cylinder radius for dynamic reaction force groups (nm)
> pull_r1  = 
> ; Switch from r1 to r0 in case of dynamic reaction force
> pull_r0  = 
> pull_constr_tol  = 1e-06
> pull_start   = no
> pull_nstxout = 10
> pull_nstfout = 10
> ; Number of pull groups 
> pull_ngroups = 700
> ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)
> pull_group0  = 
> pull_weights0= 
> pull_pbcatom0= 
> pull_group1  = sla
> pull_weights1= 1
> pull_pbcatom1= 0
> pull_vec1= 0.0 0.0 1.0
> pull_init1   = 0.0
> pull_rate1   = 0
> pull_k1  = 1.2e-4
> pull_kB1 = 0
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[gmx-users] About "Apply Multiple bonded interactions" for dihedral potential definition

[WU Yanbin]

Hi, all,

According to Manual v3.3, "It's possible to apply multiple bonded
interactions of the same type on the same atoms" [12th line of Page 98].
If a dihedral potential for 4 neighboring atoms is defined 3 times using the
"periodic type" in the topology file, like
V=k1*(1+cos(phi-phi_s1))
V=k2*(1+cos(2*phi-phi_s2))
V=k3*(1+cos(3*phi-phi_s3))
would GROMACS recognize the dihedral potential as the sum of the above
three, or just the 3rd one (which is defined last)?
If GROMACS recognizes the dihedral potential as the sum, then this can be
another way to define OPLS force filed in GROMACS.
Does anyone know the answer? Thanks.

Best,
Yanbin
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Re: [gmx-users] Re: Steered Molecular Dynamics (SMD) in Gromcas-4.0.5(toby10222...@sina.com)

[Justin A. Lemkul]

toby10222...@sina.com wrote:

Hi Carsten:

Thank you for your answers. I don't know whether I am right to reply to 
gmx-users@gromacs.org . If I am wrong, 
please tell me.




Yes, keep all discussions on the list for archival purposes (plus, other users 
can weigh in with advice).


As in my last letter, I said I was not able to set "*pull_weights1*" 
correctly. I have red the mannual, but I don't understand what it tells. 
I'll do with your recommendation, setting one pull group which contains 
700 atoms and using Gromacs-4.0.7. Then how to set the "*pull_weights1*" ?




If you have a single pull group with 700 atoms, then you can leave pull_weights1 
alone - leave it to its default value (which I believe is 0) by not even 
specifying it in the .mdp file.


-Justin


Best regards!

 

 


Hi,

you should set one pull group, not 700. The number of atoms in your
pull group is 700. Freezing the pull group in x and y direction probably
does what you want. Please also consider to upgrade to 4.0.7,
which is the most recent stable version.

Best,
  Carsten


On Jan 22, 2010, at 7:41 AM, toby10222...@sina.com wrote:

 > Dear all:
 >I’m using Gromacs-4.0.5 and I want to use the pull code to pull a 
slab of griphene to move along the Z direction in the simulation (Steered 
Molecular Dynamics-SMD). The griphene has 700 carbon atoms and the positions of 
the 700 atoms are expected to be immobile in the X and Y direction.
 > The following is the PULL CODE in my mdp file. However, when I used this 
code for my simulation the error always came out as “Number of weights (1) for 
pull group 1 'sla' does not match the number of atoms (700)”.
 > So here are my doubts about this simulation:
 > 1.   Can Gromacs-4.0.5 do this for me, especially keeping the C atoms 
immobile in X and Y direction while moving along the Z direction?
 > 2.   In my simulation, every carbon atom in the slab of griphene was 
defined as a group. Is it right?
 > 3.   How to give the “pull_weights1” to avoid the above ERROR?
 > Any suggestions and answers are welcome. Thank you in advance!
 >  
 > ; COM PULLING  
 > ; Pull type: no, umbrella, constraint or constant_force

 > pull = constant_force
 > ; Pull geometry: distance, direction, cylinder or position
 > pull_geometry= distance
 > ; Select components for the pull vector. default: Y Y Y
 > pull_dim = N N Y
 > ; Cylinder radius for dynamic reaction force groups (nm)
 > pull_r1  = 
 > ; Switch from r1 to r0 in case of dynamic reaction force
 > pull_r0  = 
 > pull_constr_tol  = 1e-06

 > pull_start   = no
 > pull_nstxout = 10
 > pull_nstfout = 10
 > ; Number of pull groups 
 > pull_ngroups = 700

 > ; Group name, weight (default all 1), vector, init, rate (nm/ps), 
kJ/(mol*nm^2)
 > pull_group0  = 
 > pull_weights0= 
 > pull_pbcatom0= 
 > pull_group1  = sla

 > pull_weights1= 1
 > pull_pbcatom1= 0
 > pull_vec1= 0.0 0.0 1.0
 > pull_init1   = 0.0
 > pull_rate1   = 0
 > pull_k1  = 1.2e-4
 > pull_kB1 = 0



--


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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