Re: [gmx-users] Regarding trajectory file

[aiswarya pawar]

You can write this on VMD forum. Anyways you can try by doing this in the
Tcl console-

set sel [atomselect top "solvent"]
$sel get {x y z}

This would give you the coordinates of the solvent, for your purpose you
got to iterate so as to get  for each time step.


Aiswarya
SERC Dept, IISc
Bangalore



On Wed, Jan 18, 2012 at 12:06 PM, Mark Abraham wrote:

> On 18/01/2012 5:31 PM, Ravi Kumar Venkatraman wrote:
>
>>
>> Dear All,
>> I have ran a 10 ns production run for chloranil in 500
>> methanol solvent box. I want to get the coordinates of solvent and solute
>> at different time steps from the trajectory file (*.xtc). Can anybody tell
>> me how to extract the details using VMD or any other viewer.
>>
>
> You're unlikely to get help for non-GROMACS software on this mailing list.
> Check out manual section 7.4 for clues on what GROMACS tools might help,
> and then section 8 and appendix D for more details.
>
> Mark
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Re: [gmx-users] Regarding trajectory file

[Mark Abraham]

On 18/01/2012 5:31 PM, Ravi Kumar Venkatraman wrote:


Dear All,
 I have ran a 10 ns production run for chloranil in 500 
methanol solvent box. I want to get the coordinates of solvent and 
solute at different time steps from the trajectory file (*.xtc). Can 
anybody tell me how to extract the details using VMD or any other viewer.


You're unlikely to get help for non-GROMACS software on this mailing 
list. Check out manual section 7.4 for clues on what GROMACS tools might 
help, and then section 8 and appendix D for more details.


Mark
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[gmx-users] Regarding trajectory file

[Ravi Kumar Venkatraman]

Dear All,
 I have ran a 10 ns production run for chloranil in 500
methanol solvent box. I want to get the coordinates of solvent and solute
at different time steps from the trajectory file (*.xtc). Can anybody tell
me how to extract the details using VMD or any other viewer.

Thank you in advance

*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.

+91-9686933963.*
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Re: [gmx-users] questions on distance restraints

[Tsjerk Wassenaar]

Hi Huiwen,

Your approach seems good. Information about the distance restraints will be
printed in the log file from mdrun, or can be extracted from the .edr file.
You can also work your way through the information in the .tpr file given
by gmxdump to see if they are indeed properly defined.

Cheers,

Tsjerk

On Jan 18, 2012 1:46 AM, "NG HUI WEN"  wrote:

 Dear gmxusers,

** **

I have some questions about distance restraints that I hope you would be
able to shed some light on. Thanks in advance.

** **

I am trying to apply distance restraints to my protein. Below was what I
did:

** **

-use genrestr to create my ca_disre.itp
genrestr –f membedded_em.gro –o ca_disre.itp –disre (pop-up prompt: CA
atoms selected)

** **

-in my mdp file

I added this line near the top: 

define  = -DDISRES

** **

-my  top file looks like that

; Include forcefield parameters

#include "gromos53a6_lipid.ff/forcefield.itp"

** **

;Include Protein Topology

#include "A2a.itp"

** **

; Include Position restraint file

#ifdef DISRES

#include "ca_disre.itp"

#endif

;

#ifdef POSRES

#include "posre.itp"

#endif

;

** **

;Include POPC topology

#include "popc.itp"

#ifdef LIPID_POSRES

#include "lipid_posre.itp"

#endif

** **

;Include water topology

#include "gromos53a6_lipid.ff/spc.itp"

** **

#ifdef POSRES_WATER

; Position restraint for each water oxygen

[ position_restraints ]

;  i funct   fcxfcyfcz

   11   1000   1000   1000

#endif

** **

; Include topology for ions

#include "gromos53a6_lipid.ff/ions.itp"

** **

[ system ]

; Name

Protein and POPC and Water 

** **

[ molecules ]

; Compound#mols

Protein_chain_X 1

POPC  327

SOL 24767

CL  11

** **

The simulation ran without a problem. However, after it was completed, I
compared the final protein structure with the initial and it looked like
the atoms (even the CA atoms , especially those in the loops) had moved
quite a fair bit away from the original position. This made me wonder if
the distance restraints had indeed been applied or perhaps the force
constant was not large enough (default =1000 kJ/mol/nm^2)?  I had checked
the mdout.mdp file “define  = -DDISRES” was there… wasn’t sure how else I
could check this.

** **

To test whether it was due to the latter, I had tried rerunning the
simulation for 1ns simulation with “disre_fc= 1” added to the
mdp file. This time the atoms did not move as far away as previously
observed. 

** **

I have tried google-ing for the proper way to impose distance restraints
but didn’t find my searches too useful. I wonder if anyone could confirm
with me that the above method is correct/ tell me that I had done something
wrong.

** **

Cheers for that!

** **

Best wishes,

Huiwen

 

** **

** **
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Re: [gmx-users] GROMOS 53A6 AND charmm36.ff

[Justin A. Lemkul]

Magnus Andersson wrote:

Hi all,

I want to use the GROMOS 53A6 forcefield for the protein, water, ions. For the membrane I intend to use charmm36.ff. 


I downloaded the charmm36.ff and put the folder as a sub-folder in 
/sw/share/gromacs/top/ as suggested in the GROMACS manual.

When I go:

pdb2gmx -f test.pdb -o -p -i -ignh -ff charmm

I get:

Fatal error:
Library file ffcharmm.ff.rtp not found in current dir nor in default 
directories.

So, I renamed "lipids.rtp" in the charmm36.ff folder to "fflipids.rtp" and 
moved the file into /sw/share/gromacs/top/

and now I get around that issue, but get a new error message:

Fatal error:
Library file fflipids.atp not found in current dir nor in default directories.



It seems like you're using an old (pre-4.5) version of Gromacs.  The force field 
organization is completely different, so what you're trying to do won't work 
unless you upgrade to a new version.



And it's not obvious to me which of the files in the charmm36.ff folder this 
corresponds to?

I guess my question is how to use pdb2gmx with he GROMOS 53A6 forcefield AND 
the charmm36.ff forcefield?



You can't.  The functional forms, representations of atoms, combination rules, 
etc. are different.  Even if you could somehow hack the force fields together to 
make it "work," I would suspect any reviewer would immediately throw out the 
results in the absence of some pretty impressive demonstration that what you're 
trying to do will actually give a reasonable physical model.


-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] GROMOS 53A6 AND charmm36.ff

[Magnus Andersson]

Hi all,

I want to use the GROMOS 53A6 forcefield for the protein, water, ions. For the 
membrane I intend to use charmm36.ff. 

I downloaded the charmm36.ff and put the folder as a sub-folder in 
/sw/share/gromacs/top/ as suggested in the GROMACS manual.

When I go:

pdb2gmx -f test.pdb -o -p -i -ignh -ff charmm

I get:

Fatal error:
Library file ffcharmm.ff.rtp not found in current dir nor in default 
directories.

So, I renamed "lipids.rtp" in the charmm36.ff folder to "fflipids.rtp" and 
moved the file into /sw/share/gromacs/top/

and now I get around that issue, but get a new error message:

Fatal error:
Library file fflipids.atp not found in current dir nor in default directories.

And it's not obvious to me which of the files in the charmm36.ff folder this 
corresponds to?

I guess my question is how to use pdb2gmx with he GROMOS 53A6 forcefield AND 
the charmm36.ff forcefield?

Best regards /

Magnus Andersson

===
Magnus Andersson, PhD
Department of Physiology and Biophysics
University of California, Irvine
Irvine, CA 92697-4560
(949) 824-6993
Fax: (949) 824-8540
===





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[gmx-users] questions on distance restraints

[NG HUI WEN]

Dear gmxusers,

I have some questions about distance restraints that I hope you would be able 
to shed some light on. Thanks in advance.

I am trying to apply distance restraints to my protein. Below was what I did:


-use genrestr to create my ca_disre.itp
genrestr -f membedded_em.gro -o ca_disre.itp -disre (pop-up prompt: CA atoms 
selected)

-in my mdp file
I added this line near the top:
define  = -DDISRES

-my  top file looks like that
; Include forcefield parameters
#include "gromos53a6_lipid.ff/forcefield.itp"

;Include Protein Topology
#include "A2a.itp"

; Include Position restraint file
#ifdef DISRES
#include "ca_disre.itp"
#endif
;
#ifdef POSRES
#include "posre.itp"
#endif
;

;Include POPC topology
#include "popc.itp"
#ifdef LIPID_POSRES
#include "lipid_posre.itp"
#endif

;Include water topology
#include "gromos53a6_lipid.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "gromos53a6_lipid.ff/ions.itp"

[ system ]
; Name
Protein and POPC and Water

[ molecules ]
; Compound#mols
Protein_chain_X 1
POPC  327
SOL 24767
CL  11

The simulation ran without a problem. However, after it was completed, I 
compared the final protein structure with the initial and it looked like the 
atoms (even the CA atoms , especially those in the loops) had moved quite a 
fair bit away from the original position. This made me wonder if the distance 
restraints had indeed been applied or perhaps the force constant was not large 
enough (default =1000 kJ/mol/nm^2)?  I had checked the mdout.mdp file "define  
= -DDISRES" was there... wasn't sure how else I could check this.

To test whether it was due to the latter, I had tried rerunning the simulation 
for 1ns simulation with "disre_fc= 1" added to the mdp file. This 
time the atoms did not move as far away as previously observed.

I have tried google-ing for the proper way to impose distance restraints but 
didn't find my searches too useful. I wonder if anyone could confirm with me 
that the above method is correct/ tell me that I had done something wrong.

Cheers for that!

Best wishes,
Huiwen



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

This message has been checked for viruses but the contents of an attachment may 
still contain software viruses which could damage your computer system: you are 
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[gmx-users] COMETS 2012 - 3rd IEEE Track on Collaborative Modeling and Simulation - Call for Papers

[Daniele Gianni]

(Please accept our apologies if you receive multiple copies of this message)

#
   IEEE WETICE 2012
 3rd IEEE Track on Collaborative Modeling and Simulation
(Comets 2012)

  in cooperation with
  AFIS (INCOSE France Chapter)
   MIMOS (Italian Association for M&S)

   CALL FOR PAPERS

#

June 25-27, 2012, Toulouse (France)
http://www.sel.uniroma2.it/comets12

#
# Papers Due: March 16, 2012
# Accepted papers will be published in the conference proceedings
# by the IEEE Computer Society Press and indexed by EI.
#

Modeling and Simulation (M&S) is increasingly becoming a central
activity in the design of new systems and in the analysis of
existing systems because it enables designers and researchers to
investigate systems behavior through virtual representations. For
this reason, M&S is gaining a primary role in many industrial and
research fields, such as space, critical infrastructures,
manufacturing, emergency management, biomedical systems and
sustainable future. However, as the complexity of the
investigated systems increases and the types of investigations
widens, the cost of M&S activities increases for the more
complex models and for the communications among a wider number and
variety of M&S stakeholders (e.g., sub-domain experts, simulator
users, simulator engineers, and final system users). To address
the increasing costs of M&S activities, collaborative
technologies must be introduced to support these activities by
fostering the sharing and reuse of models, by facilitating the
communications among M&S stakeholders, and more generally by
integrating processes, tools and platforms.

Aside from seeking applications of collaborative technologies to
M&S activities, the track seeks innovative contributions that
deal with the application of M&S practices to the design of
collaborative environments. These environments are continuously
becoming more complex, and therefore their design requires
systematic approaches to meet the required quality of
collaboration. This is important for two reasons: to reduce
rework activities on the actual collaborative environment, and to
maximize the productivity and the quality of the process the
collaborative environment supports. M&S offers the methodologies
and tools for such investigations and therefore it can be used to
improve the quality of collaborative environments.

A non–exhaustive list of topics of interest includes:

* collaborative environments for M&S
* collaborative Systems of Systems M&S
* workflow modelling for collaborative environments and processes
* agent-based M&S
* collaborative distributed simulation
* collaborative component-based M&S
* net-centric M&S
* web-based M&S
* model sharing and reuse
* model building and evaluation
* modeling and simulation of business processes
* modeling for collaboration
* simulation-based performance evaluation of collaborative networks
* model-driven simulation engineering
* domain specific languages for the simulation of collaborative environments
* domain specific languages for collaborative M&S
* databases and repositories for M&S
* distributed virtual environments
* virtual research environment for M&S
* collaborative DEVS M&S

To stimulate creativity, however, the track maintains a wider
scope and invites interested researchers to present contributions
that offer original perspectives on collaboration and M&S.

+++
On-Line Submissions and Publication
+++

CoMetS'12 intends to bring together researchers and practitioners
to discuss key issues, approaches, open problems, innovative
applications and trends in the track research area.

This year, we will accept submissions in two forms:

(1) papers
(2) poster and industrial presentations

(1) Papers should contain original contributions not published or
submitted elsewhere. Papers up to six pages (including figures,
tables and references) can be submitted. Papers should follow the
IEEE format, which is single spaced, two columns, 10 pt
Times/Roman font. All submissions should be electronic (in PDF)
and will be peer-reviewed by at least three program committee
members.

Accepted full papers will be included in the proceedings and
published by the IEEE Computer Society Press (IEEE approval pending).
Please note that at least one author for each accepted paper should
register to attend WETICE 2012 (http://www.wetice.org) to have the
paper published in the proceedings.

(2) Posters should describe a practical, on-the-field, experience in
any domain area using collaborative M&S. The poster submission
requires the submission of an abstract for e

Re: [gmx-users] Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values

[aiswarya pawar]

Yes it worked. Thanks :)

On Tue, Jan 17, 2012 at 10:26 PM, Justin A. Lemkul  wrote:

>
>
> aiswarya pawar wrote:
>
>> Hi users,
>>
>> Am trying to run the grimaces gpu version. I receive an error while doing
>> the nvt step . my nvt.mdp file goes like this=
>>
>> ; VARIOUS PREPROCESSING OPTIONS
>> title= NVT simulation (constant number, volume and
>> temperature)
>> cpp  = /lib/cpp
>>
>> ; RUN CONTROL PARAMETERS
>> integrator   = md
>> dt   = 0.002
>> nsteps   = 1250
>>
>> ; OUTPUT CONTROL OPTIONS
>> nstxout  = 0; No output, except for
>> last frame (coordinates)
>> nstvout  = 0; No output, except for
>> last frame (velocities)
>> nstfout  = 0; No output, except for
>> last frame (forces)
>> nstlog   = 1; Write every step to the
>> log nstenergy= 5; Write energies at
>> every step
>> nstxtcout= 0; Do not write a
>> compressed trajectory
>> energygrps   = System   ; Write energy
>> information separately for these groups
>>
>> ; NEIGHBORSEARCHING PARAMETERS
>> nstlist  = 5
>> ns-type  = Grid
>> pbc  = xyz
>> rlist= 0.9
>>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>> coulombtype  = PME
>> rcoulomb = 0.9
>> epsilon_rf   = 54
>> vdw-type = Cut-off
>> rvdw = 1.4
>>
>> ; Temperature coupling  tcoupl   = Berendsen
>> tc-grps  = System
>> tau_t= 0.1  0.1
>> ref_t= 300  300
>>
>> ; Pressure coupling pcoupl   = no
>>
>> ; OPTIONS FOR BONDSconstraints  = hbonds
>>
>>
>> i get an error as "Invalid T coupling input: 1 groups, 2 ref_t values and
>> 2 tau_t values"
>>
>> please tell me whats wrong.
>>
>>
> Precisely what it says.  You specify one group to be coupled (System), but
> then provide coupling information for two groups.
>
> -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] query about identifying representative snapshots from a 2D FEL

[R.S.K.Vijayan]

Dear Gromacs users

I am interested in identifying the representative snapshots from a 2D Free
energy landscape plot  generated using g_sham using  the  reaction
coordinates obtained from EV1 and EV2  projections.

Can some suggest  on how to back trace  the coordinates from a 2D FEL and
also the time.

To be more precise i want to carry out an analysis exactly like what has
been reported in Figure 8 of this refereed paper

http://pubs.rsc.org/en/content/articlehtml/2011/cp/c0cp02697b

Your suggestions would be greatly appreciated

Thanking you in advance



Regards
Vijayan.R
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[gmx-users] walls

[mohammad agha]

Dear Gromacs users,

May I ask you to help me about use of walls in martini coarse-grained, please?
I defined two walls for my system as following:
pbc        = xy         
nwall  = 2
wall_type    = 12_6
wall_r_linpot    = 1
wall_atomtype = W  W
I selected water as wall_atomtype, when I run grompp, all of things are good, 
but when I run mdrun, system give me: Segmentation fault
If I use pbc=xyz without walls, all of things are good, then my problem is wall.

May I know my mistake, please?
    

Best Regards
Sara
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Re: [gmx-users] Abot genbox and editcon

[Justin A. Lemkul]

vidhya sankar wrote:

Dear justin Thank you for your previous reply

  I have solvated  my 
protein molecule with specific number of water molecules By keeping the 
protein (solute) at center of box (option available in editconf)  but 
when i visualize the resultant  .gro file in VMD  the solute molecule 
are not closely surrounded by  water molecules i need Solute  molecules 
to be  closely surrounded by  solvent molecules  without changing the 
dimension of box i am using Cubic box is there is any option in 
available in gromacs


No - genbox works by tiling the given solvent coordinate file into the solute 
coordinate file starting at the coordinate origin.  You could randomly insert 
individual water molecules with -ci -nmol, but you'll still end up with 
significant voids akin to the gas phase, or more likely something that doesn't 
even make sense.


-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] Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values

[Justin A. Lemkul]

aiswarya pawar wrote:

Hi users,

Am trying to run the grimaces gpu version. I receive an error while 
doing the nvt step . my nvt.mdp file goes like this=


; VARIOUS PREPROCESSING OPTIONS
title= NVT simulation (constant number, volume and 
temperature)

cpp  = /lib/cpp

; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002
nsteps   = 1250

; OUTPUT CONTROL OPTIONS
nstxout  = 0; No output, except for 
last frame (coordinates)
nstvout  = 0; No output, except for 
last frame (velocities)
nstfout  = 0; No output, except for 
last frame (forces)
nstlog   = 1; Write every step to 
the log 
nstenergy= 5; Write energies at 
every step
nstxtcout= 0; Do not write a 
compressed trajectory
energygrps   = System   ; Write energy 
information separately for these groups


; NEIGHBORSEARCHING PARAMETERS
nstlist  = 5
ns-type  = Grid
pbc  = xyz
rlist= 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = PME
rcoulomb = 0.9
epsilon_rf   = 54
vdw-type = Cut-off
rvdw = 1.4

; Temperature coupling  
tcoupl   = Berendsen

tc-grps  = System
tau_t= 0.1  0.1
ref_t= 300  300

; Pressure coupling 
pcoupl   = no


; OPTIONS FOR BONDS
constraints  = hbonds



i get an error as "Invalid T coupling input: 1 groups, 2 ref_t values 
and 2 tau_t values"


please tell me whats wrong.



Precisely what it says.  You specify one group to be coupled (System), but then 
provide coupling information for two groups.


-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] Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values

[aiswarya pawar]

Hi users,

Am trying to run the grimaces gpu version. I receive an error while doing
the nvt step . my nvt.mdp file goes like this=

; VARIOUS PREPROCESSING OPTIONS
title= NVT simulation (constant number, volume and
temperature)
cpp  = /lib/cpp

; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002
nsteps   = 1250

; OUTPUT CONTROL OPTIONS
nstxout  = 0; No output, except for
last frame (coordinates)
nstvout  = 0; No output, except for
last frame (velocities)
nstfout  = 0; No output, except for
last frame (forces)
nstlog   = 1; Write every step to the
log
nstenergy= 5; Write energies at every
step
nstxtcout= 0; Do not write a compressed
trajectory
energygrps   = System   ; Write energy information
separately for these groups

; NEIGHBORSEARCHING PARAMETERS
nstlist  = 5
ns-type  = Grid
pbc  = xyz
rlist= 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = PME
rcoulomb = 0.9
epsilon_rf   = 54
vdw-type = Cut-off
rvdw = 1.4

; Temperature coupling
tcoupl   = Berendsen
tc-grps  = System
tau_t= 0.1  0.1
ref_t= 300  300

; Pressure coupling
pcoupl   = no

; OPTIONS FOR BONDS
constraints  = hbonds


i get an error as "Invalid T coupling input: 1 groups, 2 ref_t values and 2
tau_t values"

please tell me whats wrong.

Thanks
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[gmx-users] Abot genbox and editcon

[vidhya sankar]

Dear justin Thank you for your previous reply

  I have solvated  my protein 
molecule with specific number of water molecules By keeping the protein 
(solute) at center of box (option available in editconf)  but when i visualize 
the resultant  .gro file in VMD  the solute molecule are not closely surrounded 
by  water moleculesi need Solute  molecules to be  closely surrounded by  
solvent molecules without changing the dimension of box i am using Cubic box is 
there is any option in available in gromacs
With Cheers
S.vidhyasankar
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Re: [gmx-users] Cytochrom C

[Justin A. Lemkul]

Dariush Mohammadyani wrote:

Dear Justin,

You are right, I had some warning and with -missing I override them, e.g.:

WARNING: atom HA is missing in residue HEM 105 in the pdb file
WARNING: atom HB is missing in residue HEM 105 in the pdb file
...

30 missing atoms. I did not know how should figure them out. I am using 
GROMACS 4.5.3

and charmm27.ff.
Cytochrome C is a difficult protein to simulate :(



You'll make your life more difficult by overriding error messages you don't 
understand ;)


If all of the missing atoms are hydrogens, then a suitable .hdb entry must be 
constructed for the heme group so that the H atoms are all rebuilt. 
Alternatively, you can add them with some external modeling software capable of 
such tasks.  If there are other missing atoms, they too need to be added.  You 
must begin with an intact model, or otherwise have the ability to produce one.


-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] Cytochrom C

[Dariush Mohammadyani]

Dear Justin,

You are right, I had some warning and with -missing I override them, e.g.:

WARNING: atom HA is missing in residue HEM 105 in the pdb file
WARNING: atom HB is missing in residue HEM 105 in the pdb file
...

30 missing atoms. I did not know how should figure them out. I am using
GROMACS 4.5.3
and charmm27.ff.
Cytochrome C is a difficult protein to simulate :(

Thanks,
Dariush





On Tue, Jan 17, 2012 at 10:33 AM, Justin A. Lemkul  wrote:

>
>
> Dariush Mohammadyani wrote:
>
>> According your help and "pdb2gmx -his -missing" I could create input
>> files. Also I used grompp without error. However, for mdrun I got this
>> error:
>>
>
> Using the -missing flag is very dangerous.  If you're using it to override
> warnings or errors that pdb2gmx is giving, your simulations will almost
> certainly be junk because the topology is broken.
>
>  *Function type CMAP Dih. not implemented in ip_pert*
>>
>>
>> How can I figure it out?
>>
>>
> Without seeing your .mdp file and knowing which Gromacs version you're
> using, there's little anyone can do to help you.  The error suggests you're
> trying to transform a CMAP dihedral using the free energy code, which
> cannot be done (per the error message).
>
>
> -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
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
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Re: [gmx-users] Re: Problem with trjconv and centering bilayer.

[Justin A. Lemkul]

Ioannis Beis wrote:

Quoting gmx-users-requ...@gromacs.org:



Message: 2
Date: Mon, 16 Jan 2012 13:38:11 -0500
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] Problem with trjconv and centering bilayer.
To: Discussion list for GROMACS users 
Message-ID: <4f146e93.4090...@vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed



Ioannis Beis wrote:

Dear gromacs users,

I am trying to center the trajectory of a bilayer in the rectangular
simulation box in the frame of my effort to calculate the bilayer
thickness with g_dist. According to the visualization, the upper layer
of the membrane lies on the lowest part of the box and the lower part of
the membrane on the highest part of the box, with the water in the
middle. There should not be anything wrong with drifting along the
z-axis, since the initial structure was at the very bottom of the box,
so even a small drift downwards -due to the pbc- would place the lower
part of the membrane on the top of the box.

I tried issuing:

trjconv -f my_trajectory.xtc -s my_initial_structure.gro -o
my_trajectory_no_jump.xtc -pbc nojump

with 0 (for system) and subsequently

trjconv -f my_trajectory_no_jump.xtc -s DOPC_1DOG.tpr -o
my_trajectory_no_jump_center.xtc -center -boxcenter tric -pbc mol

with 1 (other) for centering and 0 (system) for output.

I used this kind of commands some time ago and they worked fine. Now
strangely the bilayer remains around the position that I described in
the beginning. Is it possible that the program treats the bilayer
separated as it looks in vmd and considers the geometrical center in the
middle of the water instead of the middle of the bilayer?



That's exactly what it does.


I tried the -trans flag to translate the bilayer along z-axis near the
center and repeated the steps, but the new trajectory wasn't even
visible in vmd. In addition, the .gro files generated by trjconv are
apparently trajectory files instead of structure files. I don't feel
confident about using editconf for operations like translation of a
single initial structure, because as far as I understand editconf is a
tool meant mostly for setting up systems; thus I was sceptical about
messing a structure with editconf that I would later on use together
with an .xtc file as input for trjconv.  However, trjconv doesn't seem
to generate structure output files. I don't understand the meaning of a
.gro file as trajectory file since there are already at least 3 file
formats for trajectories.



Generally speaking, a trajectory is just a series of coordinates, so 
you can
output it into a number of formats, including .gro and .pdb, among  
others.  You
get a chain of coordinate files that may (or may not) end up being 
useful in

some applications.


So how can I bring my bilayer's trajectory in the center of the unit
cell for reliable thickness calculation without drifts? Is it possible
at the same time to have clear visualization without disturbances?
trjconv with -pbc mol still gives rise to lines in the visualization,
apparently as a result of atom jumps. Sadly trajectory files cannot be
inspected and visualization is quite handy for certain types of feedback
in various data analysis-related tasks, so it would be nice if the
trajectories used for analysis also look proper in vmd.



I can think of two approaches, the first of which I have used so it  
should work ;)


1. Provide a custom index group specifying only a single lipid atom  
from the end
of a hydrocarbon chain and center on it.  Therefore, its geometric  
center has to
be the center of the box, and it should bring the rest of the membrane 
to the

(visual) center of the unit cell.

2. Calculate the distance with the trajectory you have now, and  
subtract it from
the z-length (assuming the membrane plane is x-y) of the box (stored 
 in the .edr

file).


First of all thank you very much for the reply. To make sure there is 
not something that I misunderstand about how trjconv works, I would like 
to mention what I did and how I anticipate it.


I made the index file with a last carbon from a random acyl chain and 
issued:


trjconv -f my_init_traj.xtc -o towards_center_traj.xtc -pbc mol -center 
-boxcenter tric -n tip_atom.ndx




How did this work?  The use of -pbc implies the need for -s.


with centering at the index file atom and then:

trjconv -f towards_center_traj.xtc -s my_binary.tpr -o centered_traj.xtc 
-pbc mol -center -boxcenter tric




If properly centered, this step should not be required.

with centering at the middle of the bilayer. The final .xtc output is to 
be used as input in the g_dist.


I assume that .tpr is used only for the masses of the atoms (so we are 
talking about a mass-weighted geometrical center, which isn't mentioned 
in the manual). Therefore it is mandatory in the second command, but not 
in the first. Is this going to give the correct result?




Masses are not used for centering; it is a simple coordinate transformation. 
See the center_x routine in gmx_t

[gmx-users] non-bonded [exclusions] / [ pairs ] for 56A_CARBO implementation

[Jon Kapla]

Hi,

I'm still a bit confused about the [ pairs ] and [ exclusions ] sections 
of an .itp file. How would the procedure be if I want to change the 
Lennard-Jones parameters for certain pairs of atoms in a molecule? The 
reason I ask is that I have created a trehalose topology based on the 
56A_CARBO (Hansen & Hünenberger, 2011) parameters, but I'm a bit unsure 
that I got the special 1-5 and and 1-4 pair right. This is how I did it 
(the modified forcefield is G53A6 or G54A7):


1. Excluded the pairs by putting them in the [ exclusions ] section
2. Added the excluded pairs in the [ pairs ] section with function type 
1 followed by the C6 and C12 parameters.


Something like this:

[ exclusions ]
15
[ pairs ]
;ft   C6C12
15 1   0.22617E-020.74158E-06

Is the choice of function right? In the manual it looks like I could 
also use function type 3 here. What is more correct?


Regards
Jon Kapla

--
_

Jon Kapla
  Division of Physical Chemistry
  Dpt. of Materials and Environmental Chemistry (MMK)
  Arrhenius Laboratory
  Stockholm University
  SE-106 91 Stockholm
Pos:PhD Student
Phone:  +46 8 16 11 79 (office)
Phone:  +46 70 304 19 89 (cell)
E-mail: jon.ka...@mmk.su.se
_

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[gmx-users] Can I fix atoms and apply load to another atoms?

[Talal E. AlOtaibi]

Hi guys,
 
I have question about gromacs.
I am doing SMD using gromacs and I don't know if gromacs can do this 
simulation: fixing atoms and applying load to another atoms at the same time?
 
if yes how, if no what another programs can do it?
 
Thanks,
Talal

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Re: [gmx-users] Cytochrom C

[Justin A. Lemkul]

Dariush Mohammadyani wrote:
According your help and "pdb2gmx -his -missing" I could create input 
files. Also I used grompp without error. However, for mdrun I got this 
error:  



Using the -missing flag is very dangerous.  If you're using it to override 
warnings or errors that pdb2gmx is giving, your simulations will almost 
certainly be junk because the topology is broken.



*Function type CMAP Dih. not implemented in ip_pert*

How can I figure it out?



Without seeing your .mdp file and knowing which Gromacs version you're using, 
there's little anyone can do to help you.  The error suggests you're trying to 
transform a CMAP dihedral using the free energy code, which cannot be done (per 
the error message).


-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] Cytochrom C

[Dariush Mohammadyani]

According your help and "pdb2gmx -his -missing" I could create input files.
Also I used grompp without error. However, for mdrun I got this error:

*Function type CMAP Dih. not implemented in ip_pert*

How can I figure it out?

Thanks,
Dariush


On Tue, Jan 10, 2012 at 4:37 PM, Krzysztof Kuczera  wrote:

>  Hi Dariush
> If you are using the CHARMM27 force field, then all topology and parameters
> are in your share/top/charmm27.ff directory
> The defined molecules are listed in aminoacids.rtp and force field
> parameters in
> numerous other files.  CHARMM does not use 'HIS' for histidine, but has
> HSD, HSE and HSP for the isomers with hydrogen at ND1, NE2 and both.
> You can either set these isomers by hand - by editing your PDB file or use
> the
> 'pdb2gmx -his' option for interactive definition.
>
> The bonus of keeping 'HIS' names and interactive setup is that bonds to
> heme
> iron will be generated based on the 'specbond.dat' entries, if HIS NE2
> nitrogens are close enough to the FE.
>
> Krzysztof
>
>
>
> On 1/10/12 2:40 PM, Dariush Mohammadyani wrote:
>
> Does anybody know where can I find [ HIS ] parameters?
>
> Thanks,
> Dariush
>
>
> On Sat, Jan 7, 2012 at 3:58 AM, Dariush Mohammadyani <
> d.mohammady...@gmail.com> wrote:
>
>  Dear Peter and Krzyszto,
>
> Thank you. I am following your comments. If I get any problem I will come
> back.
>
>
>
>
> On Fri, Jan 6, 2012 at 2:18 PM, Peter C. Lai  wrote:
>
> He must be using an older version of Gromacs. 4.5.4 and lower don't have
> ACE in charmm27.
>
> On 2012-01-06 12:59:56PM -0600, Krzysztof Kuczera wrote:
> > Here is the blocking group from
> > gromacs-4.5.5/share/top/charmm27.ff/aminoacids.rtp
> > KK
> >
> > [ ACE ]
> >   [ atoms ]
> >  CH3 CT3 -0.270  0
> >  HH31HA  0.090   1
> >  HH32HA  0.090   2
> >  HH33HA  0.090   3
> >  C   C   0.510   4
> >  O   O   -0.510  5
> >   [ bonds ]
> >  C   CH3
> >  C   +N
> >  CH3 HH31
> >  CH3 HH32
> >  CH3 HH33
> >  O   C
> >   [ impropers ]
> >  C   CH3 +N  O
> >
> >
> > On 1/6/12 12:40 PM, Peter C. Lai wrote:
> > > Corrected bonds section (sorry been up all night)
> > >
> > >   [ ACE ]
> > >[ atoms ]
> > >  CH3CT3-0.270
> > >  HH31 HA  0.091
> > >  HH32 HA  0.092
> > >  HH33 HA  0.093
> > >  CC   0.514
> > >  OO  -0.515
> > >[ bonds ]
> > >  CH3HH31
> > >  CH3HH32
> > >  CH3HH33
> > >  CH3C
> > >  C  O
> > >
> > >   Surprisingly, an .hdb entry for ACE exists so you don't need to
> create one.
> > > (and the .hdb entry uses HH3 as the base hydrogen name in ACE)
> > >
> > >>
> > >> On 2012-01-06 12:23:49PM -0600, Peter C. Lai wrote:
> > >>> Gromos96 53A6 has it.
> > >>>
> > >>> On 2012-01-06 01:18:38PM -0500, Dariush Mohammadyani wrote:
> >  I tried charmm27 too.
> > 
> >  Error:
> >  Residue 'ACE' not found in residue topology database
> > 
> >  I tried all forcefield in the list provided by "pdb2gmx", but non
> of them
> >  works.
> > 
> >  Dariush
> > 
> > 
> >  On Thu, Jan 5, 2012 at 1:42 PM, Robert Hamers
>  wrote:
> > 
> > > HEME is in the charmm27 force field.
> > > bob h.
> > >
> > >
> > >
> > >
> > > On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote:
> > >
> > > Yes, I have PDB file (1HRC.pdb). However, when I try to use
> "pdb2gmx" I
> > > get this error:
> > >
> > > Residue 'HEM' not found in residue topology database
> > >
> > > and HEM is Iron ion inside this protein. I do not know which
> forcefield is
> > > proper to use. I also tried MARTINI force field according their
> website; I
> > > used martinize.py script; Again I got error.
> > >
> > > Regards,
> > > Dariush
> > >
> > >
> > >
> > >
> > > On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkul
>  wrote:
> > >
> > >>
> > >> Dariush Mohammadyani wrote:
> > >>
> > >>> Hi all,
> > >>>
> > >>> Has anybody made initial configuration for Cytochrom C? Can it
> be shared
> > >>> with me?
> > >>>
> > >>>
> > >>   There are several in the PDB.
> > >>
> > >> -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 <%28540%29%20231-9080>
> > >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >>
> > >> 
> > >>
> > >> --
> > >> gmx-users mailing listgmx-u

Re: [gmx-users] grompp g96angle types error

[pithevenet]

Ok! The problem doesn't really come from gromacs so. It's my side-chain 
positioning software which made this... I'll try to fix it.

Thank you very much.

Pierre THEVEVENET


- Mail original -
De: "Justin A. Lemkul" 
À: "Discussion list for GROMACS users" 
Envoyé: Mardi 17 Janvier 2012 15:30:08
Objet: Re: [gmx-users] grompp g96angle types error



pitheve...@free.fr wrote:
> The problem seems to be between 3 S of CYS residues. I only use the 20 usual 
> residues and with no modifications.
>

An angle involving three S atoms?  That should never occur.

> Where is the ffbonded.itp file?

It's in $GMXLIB, i.e. the /share/gromacs/top subdirectory of your Gromacs
installation.  If the problematic angle is indeed S-S-S, I guarantee you won't
find it there, though.

-Justin

>
> Thank you,
>
>
> Pierre THEVENET
>
> - Mail original -
> De: "Justin A. Lemkul" 
> À: "Discussion list for GROMACS users" 
> Envoyé: Mardi 17 Janvier 2012 15:12:58
> Objet: Re: [gmx-users] grompp g96angle types error
>
>
>
> pitheve...@free.fr wrote:
>> Dear all,
>>
>> I launch those commands for few models :
>>
>> pdb2gmx  -f 2it7-10_bestene1mc-SC.pdb  -o 2it7-10_bestene1mc-SC.gro  -p 
>> 2it7-10_bestene1mc-SC.top -ignh -missing
>>
>> editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d 
>> 2.0 -c -bt cubic
>>
>> grompp -c 2it7-10_bestene1mc-SC-box.gro -p 2it7-10_bestene1mc-SC.top -o 
>> 2it7-10_bestene1mc-SC-min.tpr -f 2it7-10_bestene1mc-SC-em.mdp
>>
>> and at the grompp command I obtain :
>>
>> checking input for internal consistency...
>> calling /lib/cpp...
>> processing topology...
>> Generated 165 of the 1596 non-bonded parameter combinations
>> ERROR 0 [file "2it7-10_bestene1mc-SC.top", line 1242]:
>>   No default G96Angle types
>> Excluding 3 bonded neighbours for Protein 1
>> NOTE:
>>   System has non-zero total charge: 1.00e+00
>>
>> processing coordinates...
>> double-checking input for internal consistency...
>> renumbering atomtypes...
>> converting bonded parameters...
>> #   G96BONDS:   254
>> #  G96ANGLES:   367
>> #  PDIHS:   149
>> #  IDIHS:   108
>> #   LJ14:   436
>>
>> I don't understand the meaning of: No default G96Angle types.
>>
>> All my files are generated by the same way, with the same softwares, and the 
>> sames options. All the models are done by the same software so the .pdb file 
>> only the coordinates of the protein change for one model to another.
>>
>> Can you help me?
>>
>
> The error message indicates that angle parameters do not exist in the chosen
> force field for a certain sequence of atoms.  This would be highly unusual 
> for a
> standard protein.  Are you using any custom residues?  The error message 
> indicates the line in the .top that is causing the problem.  Look it up, find
> which atoms it corresponds to, and check ffbonded.itp to verify that suitable
> parameters are indeed not present.  If you're using some kind of custom 
> residue
> or nonstandard composition of atoms, then you'll likely have to parameterize 
> the
> missing term(s) yourself.
>
> -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: Problem with trjconv and centering bilayer.

[Ioannis Beis]

Quoting gmx-users-requ...@gromacs.org:



Message: 2
Date: Mon, 16 Jan 2012 13:38:11 -0500
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] Problem with trjconv and centering bilayer.
To: Discussion list for GROMACS users 
Message-ID: <4f146e93.4090...@vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed



Ioannis Beis wrote:

Dear gromacs users,

I am trying to center the trajectory of a bilayer in the rectangular
simulation box in the frame of my effort to calculate the bilayer
thickness with g_dist. According to the visualization, the upper layer
of the membrane lies on the lowest part of the box and the lower part of
the membrane on the highest part of the box, with the water in the
middle. There should not be anything wrong with drifting along the
z-axis, since the initial structure was at the very bottom of the box,
so even a small drift downwards -due to the pbc- would place the lower
part of the membrane on the top of the box.

I tried issuing:

trjconv -f my_trajectory.xtc -s my_initial_structure.gro -o
my_trajectory_no_jump.xtc -pbc nojump

with 0 (for system) and subsequently

trjconv -f my_trajectory_no_jump.xtc -s DOPC_1DOG.tpr -o
my_trajectory_no_jump_center.xtc -center -boxcenter tric -pbc mol

with 1 (other) for centering and 0 (system) for output.

I used this kind of commands some time ago and they worked fine. Now
strangely the bilayer remains around the position that I described in
the beginning. Is it possible that the program treats the bilayer
separated as it looks in vmd and considers the geometrical center in the
middle of the water instead of the middle of the bilayer?



That's exactly what it does.


I tried the -trans flag to translate the bilayer along z-axis near the
center and repeated the steps, but the new trajectory wasn't even
visible in vmd. In addition, the .gro files generated by trjconv are
apparently trajectory files instead of structure files. I don't feel
confident about using editconf for operations like translation of a
single initial structure, because as far as I understand editconf is a
tool meant mostly for setting up systems; thus I was sceptical about
messing a structure with editconf that I would later on use together
with an .xtc file as input for trjconv.  However, trjconv doesn't seem
to generate structure output files. I don't understand the meaning of a
.gro file as trajectory file since there are already at least 3 file
formats for trajectories.



Generally speaking, a trajectory is just a series of coordinates, so you can
output it into a number of formats, including .gro and .pdb, among   
others.  You

get a chain of coordinate files that may (or may not) end up being useful in
some applications.


So how can I bring my bilayer's trajectory in the center of the unit
cell for reliable thickness calculation without drifts? Is it possible
at the same time to have clear visualization without disturbances?
trjconv with -pbc mol still gives rise to lines in the visualization,
apparently as a result of atom jumps. Sadly trajectory files cannot be
inspected and visualization is quite handy for certain types of feedback
in various data analysis-related tasks, so it would be nice if the
trajectories used for analysis also look proper in vmd.



I can think of two approaches, the first of which I have used so it   
should work ;)


1. Provide a custom index group specifying only a single lipid atom   
from the end
of a hydrocarbon chain and center on it.  Therefore, its geometric   
center has to

be the center of the box, and it should bring the rest of the membrane to the
(visual) center of the unit cell.

2. Calculate the distance with the trajectory you have now, and   
subtract it from
the z-length (assuming the membrane plane is x-y) of the box (stored  
 in the .edr

file).


First of all thank you very much for the reply. To make sure there is  
not something that I misunderstand about how trjconv works, I would  
like to mention what I did and how I anticipate it.


I made the index file with a last carbon from a random acyl chain and issued:

trjconv -f my_init_traj.xtc -o towards_center_traj.xtc -pbc mol  
-center -boxcenter tric -n tip_atom.ndx


with centering at the index file atom and then:

trjconv -f towards_center_traj.xtc -s my_binary.tpr -o  
centered_traj.xtc -pbc mol -center -boxcenter tric


with centering at the middle of the bilayer. The final .xtc output is  
to be used as input in the g_dist.


I assume that .tpr is used only for the masses of the atoms (so we are  
talking about a mass-weighted geometrical center, which isn't  
mentioned in the manual). Therefore it is mandatory in the second  
command, but not in the first. Is this going to give the correct result?


A relevant concern is whether the -pbc flag is used properly. I just  
used the mol value assuming that is appropriate for this context (is  
it necessary?). Does it make any difference in the results if I use  
-pbc nojump or no -pbc at all in the fi

Re: [gmx-users] grompp g96angle types error

[Justin A. Lemkul]

pitheve...@free.fr wrote:

The problem seems to be between 3 S of CYS residues. I only use the 20 usual 
residues and with no modifications.



An angle involving three S atoms?  That should never occur.


Where is the ffbonded.itp file?


It's in $GMXLIB, i.e. the /share/gromacs/top subdirectory of your Gromacs 
installation.  If the problematic angle is indeed S-S-S, I guarantee you won't 
find it there, though.


-Justin



Thank you,


Pierre THEVENET

- Mail original -
De: "Justin A. Lemkul" 
À: "Discussion list for GROMACS users" 
Envoyé: Mardi 17 Janvier 2012 15:12:58
Objet: Re: [gmx-users] grompp g96angle types error



pitheve...@free.fr wrote:

Dear all,

I launch those commands for few models :

pdb2gmx  -f 2it7-10_bestene1mc-SC.pdb  -o 2it7-10_bestene1mc-SC.gro  -p 
2it7-10_bestene1mc-SC.top -ignh -missing

editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d 2.0 
-c -bt cubic

grompp -c 2it7-10_bestene1mc-SC-box.gro -p 2it7-10_bestene1mc-SC.top -o 
2it7-10_bestene1mc-SC-min.tpr -f 2it7-10_bestene1mc-SC-em.mdp

and at the grompp command I obtain : 


checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 165 of the 1596 non-bonded parameter combinations
ERROR 0 [file "2it7-10_bestene1mc-SC.top", line 1242]:
  No default G96Angle types
Excluding 3 bonded neighbours for Protein 1
NOTE:
  System has non-zero total charge: 1.00e+00

processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
#   G96BONDS:   254
#  G96ANGLES:   367
#  PDIHS:   149
#  IDIHS:   108
#   LJ14:   436

I don't understand the meaning of: No default G96Angle types.

All my files are generated by the same way, with the same softwares, and the 
sames options. All the models are done by the same software so the .pdb file 
only the coordinates of the protein change for one model to another.

Can you help me?



The error message indicates that angle parameters do not exist in the chosen 
force field for a certain sequence of atoms.  This would be highly unusual for a 
standard protein.  Are you using any custom residues?  The error message 
indicates the line in the .top that is causing the problem.  Look it up, find 
which atoms it corresponds to, and check ffbonded.itp to verify that suitable 
parameters are indeed not present.  If you're using some kind of custom residue 
or nonstandard composition of atoms, then you'll likely have to parameterize the 
missing term(s) yourself.


-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] grompp g96angle types error

[pithevenet]

The problem seems to be between 3 S of CYS residues. I only use the 20 usual 
residues and with no modifications.

Where is the ffbonded.itp file?

Thank you,


Pierre THEVENET

- Mail original -
De: "Justin A. Lemkul" 
À: "Discussion list for GROMACS users" 
Envoyé: Mardi 17 Janvier 2012 15:12:58
Objet: Re: [gmx-users] grompp g96angle types error



pitheve...@free.fr wrote:
> Dear all,
>
> I launch those commands for few models :
>
> pdb2gmx  -f 2it7-10_bestene1mc-SC.pdb  -o 2it7-10_bestene1mc-SC.gro  -p 
> 2it7-10_bestene1mc-SC.top -ignh -missing
>
> editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d 2.0 
> -c -bt cubic
>
> grompp -c 2it7-10_bestene1mc-SC-box.gro -p 2it7-10_bestene1mc-SC.top -o 
> 2it7-10_bestene1mc-SC-min.tpr -f 2it7-10_bestene1mc-SC-em.mdp
>
> and at the grompp command I obtain :
>
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 165 of the 1596 non-bonded parameter combinations
> ERROR 0 [file "2it7-10_bestene1mc-SC.top", line 1242]:
>   No default G96Angle types
> Excluding 3 bonded neighbours for Protein 1
> NOTE:
>   System has non-zero total charge: 1.00e+00
>
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> #   G96BONDS:   254
> #  G96ANGLES:   367
> #  PDIHS:   149
> #  IDIHS:   108
> #   LJ14:   436
>
> I don't understand the meaning of: No default G96Angle types.
>
> All my files are generated by the same way, with the same softwares, and the 
> sames options. All the models are done by the same software so the .pdb file 
> only the coordinates of the protein change for one model to another.
>
> Can you help me?
>

The error message indicates that angle parameters do not exist in the chosen
force field for a certain sequence of atoms.  This would be highly unusual for a
standard protein.  Are you using any custom residues?  The error message
indicates the line in the .top that is causing the problem.  Look it up, find
which atoms it corresponds to, and check ffbonded.itp to verify that suitable
parameters are indeed not present.  If you're using some kind of custom residue
or nonstandard composition of atoms, then you'll likely have to parameterize the
missing term(s) yourself.

-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] grompp g96angle types error

[Justin A. Lemkul]

pitheve...@free.fr wrote:

Dear all,

I launch those commands for few models :

pdb2gmx  -f 2it7-10_bestene1mc-SC.pdb  -o 2it7-10_bestene1mc-SC.gro  -p 
2it7-10_bestene1mc-SC.top -ignh -missing

editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d 2.0 
-c -bt cubic

grompp -c 2it7-10_bestene1mc-SC-box.gro -p 2it7-10_bestene1mc-SC.top -o 
2it7-10_bestene1mc-SC-min.tpr -f 2it7-10_bestene1mc-SC-em.mdp

and at the grompp command I obtain : 


checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 165 of the 1596 non-bonded parameter combinations
ERROR 0 [file "2it7-10_bestene1mc-SC.top", line 1242]:
  No default G96Angle types
Excluding 3 bonded neighbours for Protein 1
NOTE:
  System has non-zero total charge: 1.00e+00

processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
#   G96BONDS:   254
#  G96ANGLES:   367
#  PDIHS:   149
#  IDIHS:   108
#   LJ14:   436

I don't understand the meaning of: No default G96Angle types.

All my files are generated by the same way, with the same softwares, and the 
sames options. All the models are done by the same software so the .pdb file 
only the coordinates of the protein change for one model to another.

Can you help me?



The error message indicates that angle parameters do not exist in the chosen 
force field for a certain sequence of atoms.  This would be highly unusual for a 
standard protein.  Are you using any custom residues?  The error message 
indicates the line in the .top that is causing the problem.  Look it up, find 
which atoms it corresponds to, and check ffbonded.itp to verify that suitable 
parameters are indeed not present.  If you're using some kind of custom residue 
or nonstandard composition of atoms, then you'll likely have to parameterize the 
missing term(s) yourself.


-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] grompp g96angle types error

[pithevenet]

Dear all,

I launch those commands for few models :

pdb2gmx  -f 2it7-10_bestene1mc-SC.pdb  -o 2it7-10_bestene1mc-SC.gro  -p 
2it7-10_bestene1mc-SC.top -ignh -missing

editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d 2.0 
-c -bt cubic

grompp -c 2it7-10_bestene1mc-SC-box.gro -p 2it7-10_bestene1mc-SC.top -o 
2it7-10_bestene1mc-SC-min.tpr -f 2it7-10_bestene1mc-SC-em.mdp

and at the grompp command I obtain : 

checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 165 of the 1596 non-bonded parameter combinations
ERROR 0 [file "2it7-10_bestene1mc-SC.top", line 1242]:
  No default G96Angle types
Excluding 3 bonded neighbours for Protein 1
NOTE:
  System has non-zero total charge: 1.00e+00

processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
#   G96BONDS:   254
#  G96ANGLES:   367
#  PDIHS:   149
#  IDIHS:   108
#   LJ14:   436

I don't understand the meaning of: No default G96Angle types.

All my files are generated by the same way, with the same softwares, and the 
sames options. All the models are done by the same software so the .pdb file 
only the coordinates of the protein change for one model to another.

Can you help me?

Thanks,

Pierre THEVENET
-- 
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Re: [gmx-users] Add counter-ions using virtual atom???

[Justin A. Lemkul]

Kiwoong Kim wrote:

Hi,

I'm getting better to use Gromacs owing to many posts on this sites :) .

I have several questions about adding the counter-ions.

My system has a number of N2 molecules which has charge, -0.40484(for 
single N) X 2.

Thus, I have to add some counter-ions to make the system neutral.

However, because I'm newbie on Gromacs, I thought of several clumsy ways 
myself.


#1. Add virtual sites (virtual atoms) which has counter-ions like below.

[ atomtypes ]
; name  mass   charge  ptype  sigma  epsilon
DUM 00.80968 V0.00.0

I set the coordinates of each virtual DUM atoms to the center of N2 
molecules.


#2. using genion in Gromacs.

But, I have no idea on this. What molecules do I have to designate to 
charge plus ion using genion ??


I typed below line.
genion -s md_0_1.tpr -n index.ndx -o ton_genion.pdb -g md_0_1_genion.log 
-p topol_genion.top -np 322 -pname dum -pq 0.80968


and selected N2 molecules which is diffusing particle.

It results that the name of half of N2 molecules is changed as DUM. 
(maybe the system become neutral)

The number of N2 molecules should be fixed.
Do I have additional N2 molecule for charging using genion?? Then, what 
are the initial coordinates???


please help me

any advises would be helpful.
How can I do that??? 



I see no reason why you should do either.  For dinitrogen, which has no net 
dipole, it seems intuitive to me that both N atoms should have zero charge.


-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] On g_hbond

[Mr Bernard Ramos]

Hi everyone!
 
On this page

http://manual.gromacs.org/online/g_hbond.html

there is an option -r2 when using g_hbond. What is this r2? I can't find it in 
the Gromacs manual. option -a is the angle H-O-O, option -r is the O-O distance 
which can be switched to H-A by using the "-da no". Need help on what is -r2 
(could this be for specifying a third criterion for the for distance O-H in 
addition to the angle cut-off and O-O distance cut-off).

Thanks!
Bernard-- 
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[gmx-users] Add counter-ions using virtual atom???

[Kiwoong Kim]

Hi,

I'm getting better to use Gromacs owing to many posts on this sites :) .

I have several questions about adding the counter-ions.

My system has a number of N2 molecules which has charge, -0.40484(for
single N) X 2.
Thus, I have to add some counter-ions to make the system neutral.

However, because I'm newbie on Gromacs, I thought of several clumsy ways
myself.

#1. Add virtual sites (virtual atoms) which has counter-ions like below.

[ atomtypes ]
; name  mass   charge  ptype  sigma  epsilon
DUM 00.80968 V0.00.0

I set the coordinates of each virtual DUM atoms to the center of N2
molecules.

#2. using genion in Gromacs.

But, I have no idea on this. What molecules do I have to designate to
charge plus ion using genion ??

I typed below line.
genion -s md_0_1.tpr -n index.ndx -o ton_genion.pdb -g md_0_1_genion.log -p
topol_genion.top -np 322 -pname dum -pq 0.80968

and selected N2 molecules which is diffusing particle.

It results that the name of half of N2 molecules is changed as DUM. (maybe
the system become neutral)
The number of N2 molecules should be fixed.
Do I have additional N2 molecule for charging using genion?? Then, what are
the initial coordinates???

please help me

any advises would be helpful.
How can I do that???
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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[gmx-users] Re: Is there a way to omit particles with, q=0, from, Coulomb-/PME-calculations?

[Thomas Schlesier]

Thanks Carsten. Now i see the problem.



Hi Thomas,

Am Jan 17, 2012 um 10:29 AM schrieb Thomas Schlesier:


But would there be a way to optimize it further?
In my real simulation i would have a charged solute and the uncharged solvent 
(both have nearly the same number of particles). If i could omit the uncharged 
solvent from the long-ranged coulomb-calculation (PME) it would save much time.
Or is there a reason that some of the PME stuff is also calculated for 
uncharged particles?


For PME you need the Fourier-transformed charge grid and you get back the 
potential
grid from which you interpolate the forces on the charged atoms. The charges 
are spread
each on typically 4x4x4 (=PME order) grid points, and in this spreading only
charged atoms will take part. So the spreading part (and also the force 
interpolation part)
will become faster with less charges. However, the rest of PME (the Fourier 
transforms
and calculations in reciprocal space) are unaffected by the number of charges. 
For
this only the size of the whole PME grid matters. You could try to lower the 
number of
PME grid points (enlarge fourierspacing) and at the same time enhance the PME 
order
(to 6 for example) to keep a comparable force accuracy. You could also try to 
shift
more load to real space, which will also lower the number of PME grid points 
(g_tune_pme
can do that for you). But I am not shure that you can get large performance 
benefits
from that.

Best,
Carsten



(Ok, i know that this is a rather specical system, in so far that in most 
md-simulations the number of uncharged particles is negligible.)
Would it be probably better to move the question to the developer-list?

Greetings
Thomas



On 17/01/2012 7:32 PM, Thomas Schlesier wrote:

On 17/01/2012 4:55 AM, Thomas Schlesier wrote:

Dear all,
Is there a way to omit particles with zero charge from calculations
for Coulomb-interactions or PME?
In my calculations i want to coarse-grain my solvent, but the solute
should be still represented by atoms. In doing so the
solvent-molecules have a zero charge. I noticed that for a simulation
with only the CG-solvent significant time was spent for the PME-part
of the simulation.
If i would simulate the complete system (atomic solute +
coarse-grained solvent), i would save only time for the reduced

number

of particles (compared to atomistic solvent). But if i could omit the
zero-charge solvent from the Coulomb-/PME-part, it would save much
additional time.

Is there an easy way for the omission, or would one have to hack the
code? If the latter is true, how hard would it be and where do i have
to look?
(First idea would be to create an index-file group with all
non-zero-charged particles and then run in the loops needed for
Coulomb/PME only over this subset of particles.)
I have only experience with Fortran and not with C++.

Only other solution which comes to my mind would be to use plain
cut-offs for the Coulomb-part. This would save time required for

doing

PME but will in turn cost time for the calculations of zeros
(Coulomb-interaction for the CG-solvent). But more importantly would
introduce artifacts from the plain cut-off :(



Particles with zero charge are not included in neighbour lists used
for calculating Coulomb interactions. The statistics in the "M E G A

->F L O P S   A C C O U N T I N G" section of the .log file will show

that there is significant use of loops that do not have "Coul"
component. So already these have no effect on half of the PME
calculation. I don't know whether the grid part is similarly
optimized, but you can test this yourself by comparing timing of runs
with and without charged solvent.

Mark


Ok, i will test this.
But here is the data i obtained for two simulations, one with plain
cut-off and the other with PME. As one sees the simulation with plain
cut-offs is much faster (by a factor of 6).


Yes. I think I have seen this before for PME when (some grid cells) are
lacking (many) charged particles.

You will see that the nonbonded loops are always "VdW(T)" for tabulated
VdW - you have no charges at all in this system and GROMACS has already
optimized its choice of nonbonded loops accordingly. You would see
"Coul(T) + VdW(T)" if your solvent had charge.

It's not a meaningful test of the performance of PME vs cut-off, either,
because there are no charges.

Mark




---

With PME:

 M E G A - F L O P S   A C C O U N T I N G

RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs)
NF=No Forces

  Computing: M-Number M-Flops  % Flops
---
  VdW(T)  1132.029152   61129.574 0.1
  Outer nonbonded loop1020.997718   10209.977 0.0
  Calc Weights   16725.001338  602100.

Re: [gmx-users] Is there a way to omit particles with, q=0, from Coulomb-/PME-calculations?

[Carsten Kutzner]

Hi Thomas,

Am Jan 17, 2012 um 10:29 AM schrieb Thomas Schlesier:

> But would there be a way to optimize it further?
> In my real simulation i would have a charged solute and the uncharged solvent 
> (both have nearly the same number of particles). If i could omit the 
> uncharged solvent from the long-ranged coulomb-calculation (PME) it would 
> save much time.
> Or is there a reason that some of the PME stuff is also calculated for 
> uncharged particles?

For PME you need the Fourier-transformed charge grid and you get back the 
potential
grid from which you interpolate the forces on the charged atoms. The charges 
are spread
each on typically 4x4x4 (=PME order) grid points, and in this spreading only
charged atoms will take part. So the spreading part (and also the force 
interpolation part)
will become faster with less charges. However, the rest of PME (the Fourier 
transforms
and calculations in reciprocal space) are unaffected by the number of charges. 
For
this only the size of the whole PME grid matters. You could try to lower the 
number of
PME grid points (enlarge fourierspacing) and at the same time enhance the PME 
order 
(to 6 for example) to keep a comparable force accuracy. You could also try to 
shift
more load to real space, which will also lower the number of PME grid points 
(g_tune_pme
can do that for you). But I am not shure that you can get large performance 
benefits
from that.

Best,
   Carsten


> (Ok, i know that this is a rather specical system, in so far that in most 
> md-simulations the number of uncharged particles is negligible.)
> Would it be probably better to move the question to the developer-list?
> 
> Greetings
> Thomas
> 
> 
>> On 17/01/2012 7:32 PM, Thomas Schlesier wrote:
>>> On 17/01/2012 4:55 AM, Thomas Schlesier wrote:
> Dear all,
> Is there a way to omit particles with zero charge from calculations
> for Coulomb-interactions or PME?
> In my calculations i want to coarse-grain my solvent, but the solute
> should be still represented by atoms. In doing so the
> solvent-molecules have a zero charge. I noticed that for a simulation
> with only the CG-solvent significant time was spent for the PME-part
> of the simulation.
> If i would simulate the complete system (atomic solute +
> coarse-grained solvent), i would save only time for the reduced
>>> number
> of particles (compared to atomistic solvent). But if i could omit the
> zero-charge solvent from the Coulomb-/PME-part, it would save much
> additional time.
> 
> Is there an easy way for the omission, or would one have to hack the
> code? If the latter is true, how hard would it be and where do i have
> to look?
> (First idea would be to create an index-file group with all
> non-zero-charged particles and then run in the loops needed for
> Coulomb/PME only over this subset of particles.)
> I have only experience with Fortran and not with C++.
> 
> Only other solution which comes to my mind would be to use plain
> cut-offs for the Coulomb-part. This would save time required for
>>> doing
> PME but will in turn cost time for the calculations of zeros
> (Coulomb-interaction for the CG-solvent). But more importantly would
> introduce artifacts from the plain cut-off :(
>>> 
 Particles with zero charge are not included in neighbour lists used
 for calculating Coulomb interactions. The statistics in the "M E G A
>>> ->F L O P S   A C C O U N T I N G" section of the .log file will show
 that there is significant use of loops that do not have "Coul"
 component. So already these have no effect on half of the PME
 calculation. I don't know whether the grid part is similarly
 optimized, but you can test this yourself by comparing timing of runs
 with and without charged solvent.
 
 Mark
>>> 
>>> Ok, i will test this.
>>> But here is the data i obtained for two simulations, one with plain
>>> cut-off and the other with PME. As one sees the simulation with plain
>>> cut-offs is much faster (by a factor of 6).
>> 
>> Yes. I think I have seen this before for PME when (some grid cells) are
>> lacking (many) charged particles.
>> 
>> You will see that the nonbonded loops are always "VdW(T)" for tabulated
>> VdW - you have no charges at all in this system and GROMACS has already
>> optimized its choice of nonbonded loops accordingly. You would see
>> "Coul(T) + VdW(T)" if your solvent had charge.
>> 
>> It's not a meaningful test of the performance of PME vs cut-off, either,
>> because there are no charges.
>> 
>> Mark
>> 
>>> 
>>> 
>>> ---
>>> 
>>> With PME:
>>> 
>>> M E G A - F L O P S   A C C O U N T I N G
>>> 
>>>RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
>>>T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs)
>>>NF=No Forces
>>> 
>>>  Computing:   

[gmx-users] micelle formation

[dina dusti]

Dear Prof.

Thank you very much from your reply. 

My question about R(micelle)=(1.291)R(gyration) is that, what is cause of 
coefficient 1.29?
Yes, I saw one micelle that the tails of surfactants are into the micelle and 
heads are out of micelle visually (consist of 80 monomer). My results that I 
sent you are the results of g_rdf for tail with the center of mass of micelle 
and g_rdf for the last bead of tail to its own (for both of them I did g_rdf 
with options -b 10 -e 30, means time from micelle formation to end)  
and I sent you just the first part of file and that file is for 30 ps 
originally. My problem is about interpret for the first part of file that is 
representative of hole in the center of micelle or no, and is it our expectancy 
in gromacs?
My question about the center of mass of micelle is because of I want to know 
that is there the way for computation of radius of hole of the center of 
micelle?

Thank you very much again.


Best Regards
Dina
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[gmx-users] Re: Re: Question about "nsttcouple"

[Size Zheng]

Dear Mark,

Thank you for your quick reply. I mean if there is any way we can control the 
frequency for coupling the temperature if we still use GROMACS V4.0.7 on LINUX?

Many thanks,

Alex

On Jan 17, 2012, at 1:08 AM, gmx-users-requ...@gromacs.org wrote:

> On 17/01/2012 7:53 PM, Size Zheng wrote:
>> Dear All,
>> 
>> We are doing a simulation for ice melting in Efield with thermostat, and we 
>> would like to control the frequency for coupling the temperature by setting 
>> "nsttcouple". But we always received a warning said it was a unknown 
>> parameter during "grompp" in GROMACS V4.0.7 on LINUX. I also tried it by 
>> GROMACS V4.5.4 on my MAC OS, it was done successfully. Unfortunately, our 
>> HPC uses GROMACS V4.0.7, so it is a problem for us.
> 
> Functionality changes from version to version, and you are observing 
> that here.
> 
>> 
>> Is there anything we did incorrectly? Any suggestions?
> 
> Install a more recent version. It's (much) less than an hour's work for 
> an experienced sysadmin, and runs faster as well.
> 
> Mark

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Re: [gmx-users] Coarse Grained Cytochrom C

[XAvier Periole]

The Heme molecule is not available in the Martini web site. We have been 
working on a model but it won't be ready for release before some time. 

You could try to make you own model. 

XAvier. 

On Jan 16, 2012, at 20:34, Dariush Mohammadyani  
wrote:

> Hi all,
> Has anybody used Coarse grained model for Cytochrome C? I could create a 
> model using MARTINI forcefiels (using martinize.py script and 1HRC.pdb file), 
> but it does not have HEM and HOH groups. Can anybody help me? 
> 
> 
> Kind Regards,
> Dariush Mohammadyani
> Department of Structural Biology
> University of Pittsburgh School of Medicine
> Biomedical Science Tower 3
> 3501 Fifth Avenue
> Pittsburgh, PA 15261
> USA
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] Is there a way to omit particles with, q=0, from Coulomb-/PME-calculations?

[Thomas Schlesier]

But would there be a way to optimize it further?
In my real simulation i would have a charged solute and the uncharged 
solvent (both have nearly the same number of particles). If i could omit 
the uncharged solvent from the long-ranged coulomb-calculation (PME) it 
would save much time.
Or is there a reason that some of the PME stuff is also calculated for 
uncharged particles?
(Ok, i know that this is a rather specical system, in so far that in 
most md-simulations the number of uncharged particles is negligible.)

Would it be probably better to move the question to the developer-list?

Greetings
Thomas



On 17/01/2012 7:32 PM, Thomas Schlesier wrote:

On 17/01/2012 4:55 AM, Thomas Schlesier wrote:

Dear all,
Is there a way to omit particles with zero charge from calculations
for Coulomb-interactions or PME?
In my calculations i want to coarse-grain my solvent, but the solute
should be still represented by atoms. In doing so the
solvent-molecules have a zero charge. I noticed that for a simulation
with only the CG-solvent significant time was spent for the PME-part
of the simulation.
If i would simulate the complete system (atomic solute +
coarse-grained solvent), i would save only time for the reduced

number

of particles (compared to atomistic solvent). But if i could omit the
zero-charge solvent from the Coulomb-/PME-part, it would save much
additional time.

Is there an easy way for the omission, or would one have to hack the
code? If the latter is true, how hard would it be and where do i have
to look?
(First idea would be to create an index-file group with all
non-zero-charged particles and then run in the loops needed for
Coulomb/PME only over this subset of particles.)
I have only experience with Fortran and not with C++.

Only other solution which comes to my mind would be to use plain
cut-offs for the Coulomb-part. This would save time required for

doing

PME but will in turn cost time for the calculations of zeros
(Coulomb-interaction for the CG-solvent). But more importantly would
introduce artifacts from the plain cut-off :(



Particles with zero charge are not included in neighbour lists used
for calculating Coulomb interactions. The statistics in the "M E G A

->F L O P S   A C C O U N T I N G" section of the .log file will show

that there is significant use of loops that do not have "Coul"
component. So already these have no effect on half of the PME
calculation. I don't know whether the grid part is similarly
optimized, but you can test this yourself by comparing timing of runs
with and without charged solvent.

Mark


Ok, i will test this.
But here is the data i obtained for two simulations, one with plain
cut-off and the other with PME. As one sees the simulation with plain
cut-offs is much faster (by a factor of 6).


Yes. I think I have seen this before for PME when (some grid cells) are
lacking (many) charged particles.

You will see that the nonbonded loops are always "VdW(T)" for tabulated
VdW - you have no charges at all in this system and GROMACS has already
optimized its choice of nonbonded loops accordingly. You would see
"Coul(T) + VdW(T)" if your solvent had charge.

It's not a meaningful test of the performance of PME vs cut-off, either,
because there are no charges.

Mark




---

With PME:

 M E G A - F L O P S   A C C O U N T I N G

RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs)
NF=No Forces

  Computing: M-Number M-Flops  % Flops
---
  VdW(T)  1132.029152   61129.574 0.1
  Outer nonbonded loop1020.997718   10209.977 0.0
  Calc Weights   16725.001338  602100.048 0.6
  Spread Q Bspline  356800.028544  713600.057 0.7
  Gather F Bspline  356800.028544 4281600.343 4.4
  3D-FFT   9936400.79491279491206.35981.6
  Solve PME 18.0144001152.92211.8
  NS-Pairs2210.718786   46425.095 0.0
  Reset In Box1115.003345.000 0.0
  CG-CoM  1115.0004463345.001 0.0
  Virial  7825.000626  140850.011 0.1
  Ext.ens. Update 5575.000446  301050.024 0.3
  Stop-CM 5575.000446   55750.004 0.1
  Calc-Ekin   5575.000892  150525.024 0.2
---
  Total  97381137.440   100.0
---
 D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

  av. #atoms communicated per

Re: [gmx-users] micelle formation

[Mark Abraham]

On 17/01/2012 7:37 PM, dina dusti wrote:

Dear Specialists,

I am a beginner in grmacs and I have several questions about formation 
of micelle in gromacs. Please help me.
1- We know that there is a thermodynamic equilibrium between created 
micelle and free monomers in solvent, but I don't see this in results 
of my simulation! When I add the number of monomers, all of them are 
aggregated depend of concentration of solution in one micelle 
(spherical to cylindrical) or several micelles and always, lack of 
single monomer is the most stable state for system. also, I didn't 
find this in previous work by gromacs.  Is it the limitation of 
gramacs? Why?


It has nothing to do with GROMACS, and likely everything to do with your 
choice of model physics and the degree of convergence of the simulation.


2- What is the relation of radius of gyration with effective radius of 
spherical micelle that in many of papers have been pointed to 
R(micelle)=(1.291)R(gyration)?


I don't understand your question, or how it relates to GROMACS :)

3- Where is the center of mass of micelle in gromacs, exactly? I 
obtained rdf for tails of surfactants with center of mass of micelle 
that the first part of file is as following:( I work with martini and 
we know that sigma= 0.47 nm in L-J)

  00
 0.002  0
 0.004  0
 0.006  0
 0.008  0
  0.01  0
 0.012  0
 0.014  0
 0.016  0
 0.018  0
  0.02  0
 0.022  0
 0.024  0
 0.026  0
 0.028  0
  0.03  0
 0.032  0
 0.03491.8328
 0.036  0
 0.038  0
  0.04  0
 0.04260.1866
 0.044  0
 0.046 50.176
 0.04846.0824
  0.0542.4701
 0.05239.2663
 0.054  0
 0.05633.8578
 0.058  0
  0.0629.4943
 0.06227.6223
 0.064  0
 0.06648.7518
 0.068  0
  0.0721.6699
 0.072  0
 0.07419.3906
 0.076  0
 0.078  0
  0.0882.9561
 0.08247.3753
 0.084  0
 0.086  0
 0.088  0
  0.0939.3277
 0.092  0
 0.09412.0173
 0.09623.0438
 0.09811.0564
   0.1  0
 0.10220.4125
 0.104 19.635
 0.1069.45052
 0.1089.10376
  0.1117.5514
 0.112  0
 0.114  0
 0.1167.89139
...

...
What does it mean? Does it say me that the center of micelle is where 
the end of tails reach together. Do the tails bond in the center of 
micelle together or there is a hole according to my result and what is 
your definition in gromacs for center of mass of micelle, hole or bond 
between tails, Please?


We don't even know whether your micelles should have monomer tails in 
the center or outside, or how you generated those numbers or what they 
are. If that's a radial distribution function, then you probably want to 
choose a narrower bin width for computing it, and get a lot more samples 
to go in it.


I took rdf for last bead of tails together that the first part of file 
is as:

0  0
 0.002  0
 0.004  0
 0.006  0
 0.008  0
 ..0
 ..0
 ..0
 0.414  0
 0.416  0
 0.418  0
  0.42  0
 0.422  0
 0.424  0
 0.426  0.0577916
 0.428  0
  0.43   0.113443
and maximum g(r) is in 0.512 nm (the first peak) and in distance 0.47 
nm, g(r) is 50.3262. Can I interpret that tails are in two states 
together: bonded and non-bonded but maximum of tails are non-bonded, 
therefore, there is a hole in the center of micelle?


I don't know, but some well-chosen use of g_rdf or g_density might get 
the information you seek if it's there to be found. Make sure you 
visualize the simulation first.


Mark
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Re: [gmx-users] Question about "nsttcouple"

[Mark Abraham]

On 17/01/2012 7:53 PM, Size Zheng wrote:

Dear All,

We are doing a simulation for ice melting in Efield with thermostat, and we would like to control 
the frequency for coupling the temperature by setting "nsttcouple". But we always 
received a warning said it was a unknown parameter during "grompp" in GROMACS V4.0.7 on 
LINUX. I also tried it by GROMACS V4.5.4 on my MAC OS, it was done successfully. Unfortunately, our 
HPC uses GROMACS V4.0.7, so it is a problem for us.


Functionality changes from version to version, and you are observing 
that here.




Is there anything we did incorrectly? Any suggestions?


Install a more recent version. It's (much) less than an hour's work for 
an experienced sysadmin, and runs faster as well.


Mark
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Re: [gmx-users] Re: Is there a way to omit particles with q=0, from Coulomb-/PME-calculations?

[Mark Abraham]

On 17/01/2012 7:32 PM, Thomas Schlesier wrote:

On 17/01/2012 4:55 AM, Thomas Schlesier wrote:
> > Dear all,
> > Is there a way to omit particles with zero charge from calculations
> > for Coulomb-interactions or PME?
> > In my calculations i want to coarse-grain my solvent, but the solute
> > should be still represented by atoms. In doing so the
> > solvent-molecules have a zero charge. I noticed that for a simulation
> > with only the CG-solvent significant time was spent for the PME-part
> > of the simulation.
> > If i would simulate the complete system (atomic solute +
> > coarse-grained solvent), i would save only time for the reduced 
number

> > of particles (compared to atomistic solvent). But if i could omit the
> > zero-charge solvent from the Coulomb-/PME-part, it would save much
> > additional time.
> >
> > Is there an easy way for the omission, or would one have to hack the
> > code? If the latter is true, how hard would it be and where do i have
> > to look?
> > (First idea would be to create an index-file group with all
> > non-zero-charged particles and then run in the loops needed for
> > Coulomb/PME only over this subset of particles.)
> > I have only experience with Fortran and not with C++.
> >
> > Only other solution which comes to my mind would be to use plain
> > cut-offs for the Coulomb-part. This would save time required for 
doing

> > PME but will in turn cost time for the calculations of zeros
> > (Coulomb-interaction for the CG-solvent). But more importantly would
> > introduce artifacts from the plain cut-off :(

>Particles with zero charge are not included in neighbour lists used 
>for calculating Coulomb interactions. The statistics in the "M E G A 
- >F L O P S   A C C O U N T I N G" section of the .log file will show 
>that there is significant use of loops that do not have "Coul" 
>component. So already these have no effect on half of the PME 
>calculation. I don't know whether the grid part is similarly 
>optimized, but you can test this yourself by comparing timing of runs 
>with and without charged solvent.

>
>Mark

Ok, i will test this.
But here is the data i obtained for two simulations, one with plain 
cut-off and the other with PME. As one sees the simulation with plain 
cut-offs is much faster (by a factor of 6).


Yes. I think I have seen this before for PME when (some grid cells) are 
lacking (many) charged particles.


You will see that the nonbonded loops are always "VdW(T)" for tabulated 
VdW - you have no charges at all in this system and GROMACS has already 
optimized its choice of nonbonded loops accordingly. You would see 
"Coul(T) + VdW(T)" if your solvent had charge.


It's not a meaningful test of the performance of PME vs cut-off, either, 
because there are no charges.


Mark




--- 


With PME:

M E G A - F L O P S   A C C O U N T I N G

   RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
   T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs)
   NF=No Forces

 Computing: M-Number M-Flops  % Flops
---
 VdW(T)  1132.029152   61129.574 0.1
 Outer nonbonded loop1020.997718   10209.977 0.0
 Calc Weights   16725.001338  602100.048 0.6
 Spread Q Bspline  356800.028544  713600.057 0.7
 Gather F Bspline  356800.028544 4281600.343 4.4
 3D-FFT   9936400.79491279491206.35981.6
 Solve PME 18.0144001152.92211.8
 NS-Pairs2210.718786   46425.095 0.0
 Reset In Box1115.003345.000 0.0
 CG-CoM  1115.0004463345.001 0.0
 Virial  7825.000626  140850.011 0.1
 Ext.ens. Update 5575.000446  301050.024 0.3
 Stop-CM 5575.000446   55750.004 0.1
 Calc-Ekin   5575.000892  150525.024 0.2
---
 Total  97381137.440   100.0
---
D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

 av. #atoms communicated per step for force:  2 x 94.1

 Average load imbalance: 10.7 %
 Part of the total run time spent waiting due to load imbalance: 0.1 %


 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing: Nodes Number G-CyclesSeconds %
---
 Domain decomp. 4250  903.835  308.1 1.8
 Comm. coord.   4   1251  321.930  109.7 0.6
 Neighbor search4250

[gmx-users] Question about "nsttcouple"

[Size Zheng]

Dear All,

We are doing a simulation for ice melting in Efield with thermostat, and we 
would like to control the frequency for coupling the temperature by setting 
"nsttcouple". But we always received a warning said it was a unknown parameter 
during "grompp" in GROMACS V4.0.7 on LINUX. I also tried it by GROMACS V4.5.4 
on my MAC OS, it was done successfully. Unfortunately, our HPC uses GROMACS 
V4.0.7, so it is a problem for us.

Is there anything we did incorrectly? Any suggestions?

Many thanks,

Alex--
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[gmx-users] micelle formation

[dina dusti]

Dear Specialists,


I am a beginner in grmacs and I have several questions about formation of 
micelle in gromacs. Please help me.
1- We know that there is a thermodynamic equilibrium between created micelle 
and free monomers in solvent, but I don't see this in results of my simulation! 
When I add the number of monomers, all of them are aggregated depend of 
concentration of solution in one micelle (spherical to cylindrical) or several 
micelles and always, lack of single monomer is the most stable state for 
system. also, I didn't find this in previous work by gromacs.  Is it the 
limitation of gramacs? Why?

2- What is the relation of radius of gyration with effective radius of 
spherical micelle that in many of papers have been pointed to 
R(micelle)=(1.291)R(gyration)?
3- Where is the center of mass of micelle in gromacs, exactly? I obtained rdf 
for tails of surfactants with center of mass of micelle that the first part of 
file is as following:( I work with martini and we know that sigma= 0.47 nm in 
L-J)

  0    0
 0.002  0
 0.004  0
 0.006  0

 0.008  0
  0.01  0
 0.012  0
 0.014  0
 0.016  0
 0.018  0
  0.02  0
 0.022  0
 0.024  0
 0.026  0

 0.028  0
  0.03  0
 0.032  0
 0.034    91.8328
 0.036  0
 0.038  0
  0.04  0
 0.042    60.1866
 0.044  0
 0.046 50.176
 0.048    46.0824
  0.05    42.4701

 0.052    39.2663
 0.054  0
 0.056    33.8578
 0.058  0
  0.06    29.4943
 0.062    27.6223
 0.064  0
 0.066    48.7518
 0.068  0
  0.07    21.6699
 0.072  0
 0.074    19.3906
 0.076 
 0
 0.078  0
  0.08    82.9561
 0.082    47.3753
 0.084  0
 0.086  0
 0.088  0
  0.09    39.3277
 0.092  0
 0.094    12.0173
 0.096    23.0438
 0.098    11.0564
   0.1  0

 0.102    20.4125
 0.104 19.635
 0.106    9.45052
 0.108    9.10376
  0.11    17.5514
 0.112  0
 0.114  0
 0.116    7.89139
...



...

What does it mean? Does it say me that the center of micelle is where the end 
of tails reach together. Do the tails bond in the center of micelle together or 
there is a hole according to my result and what is your definition in gromacs 
for center of mass of micelle, hole or bond between tails, Please?  

I took rdf for last bead of tails together that the first part of file is 
as:    0  0
 0.002  0
 0.004  0
 0.006  0
 0.008  0
 ..0
 ..0
 ..0

 0.414  0
 0.416  0
 0.418  0
  0.42  0
 0.422  0
 0.424  0
 0.426  0.0577916
 0.428  0
  0.43   0.113443
and maximum g(r) is in 0.512 nm (the first peak) and in distance 0.47 nm, g(r) 
is 50.3262. Can I interpret that tails are in two states together: bonded and 
non-bonded but maximum of tails are non-bonded, therefore, there is a hole in 
the center of micelle?

Please help me.
Thank you very much in advance.

Best Regards
Dina-- 
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[gmx-users] Re: Is there a way to omit particles with q=0, from Coulomb-/PME-calculations?

[Thomas Schlesier]

On 17/01/2012 4:55 AM, Thomas Schlesier wrote:
> > Dear all,
> > Is there a way to omit particles with zero charge from calculations
> > for Coulomb-interactions or PME?
> > In my calculations i want to coarse-grain my solvent, but the solute
> > should be still represented by atoms. In doing so the
> > solvent-molecules have a zero charge. I noticed that for a simulation
> > with only the CG-solvent significant time was spent for the PME-part
> > of the simulation.
> > If i would simulate the complete system (atomic solute +
> > coarse-grained solvent), i would save only time for the reduced number
> > of particles (compared to atomistic solvent). But if i could omit the
> > zero-charge solvent from the Coulomb-/PME-part, it would save much
> > additional time.
> >
> > Is there an easy way for the omission, or would one have to hack the
> > code? If the latter is true, how hard would it be and where do i have
> > to look?
> > (First idea would be to create an index-file group with all
> > non-zero-charged particles and then run in the loops needed for
> > Coulomb/PME only over this subset of particles.)
> > I have only experience with Fortran and not with C++.
> >
> > Only other solution which comes to my mind would be to use plain
> > cut-offs for the Coulomb-part. This would save time required for doing
> > PME but will in turn cost time for the calculations of zeros
> > (Coulomb-interaction for the CG-solvent). But more importantly would
> > introduce artifacts from the plain cut-off :(

>Particles with zero charge are not included in neighbour lists used 
>for calculating Coulomb interactions. The statistics in the "M E G A - 
>F L O P S   A C C O U N T I N G" section of the .log file will show 
>that there is significant use of loops that do not have "Coul" 
>component. So already these have no effect on half of the PME 
>calculation. I don't know whether the grid part is similarly 
>optimized, but you can test this yourself by comparing timing of runs 
>with and without charged solvent.

>
>Mark

Ok, i will test this.
But here is the data i obtained for two simulations, one with plain 
cut-off and the other with PME. As one sees the simulation with plain 
cut-offs is much faster (by a factor of 6).



---
With PME:

M E G A - F L O P S   A C C O U N T I N G

   RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
   T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs)
   NF=No Forces

 Computing: M-Number M-Flops  % Flops
---
 VdW(T)  1132.029152   61129.574 0.1
 Outer nonbonded loop1020.997718   10209.977 0.0
 Calc Weights   16725.001338  602100.048 0.6
 Spread Q Bspline  356800.028544  713600.057 0.7
 Gather F Bspline  356800.028544 4281600.343 4.4
 3D-FFT   9936400.79491279491206.35981.6
 Solve PME 18.0144001152.92211.8
 NS-Pairs2210.718786   46425.095 0.0
 Reset In Box1115.003345.000 0.0
 CG-CoM  1115.0004463345.001 0.0
 Virial  7825.000626  140850.011 0.1
 Ext.ens. Update 5575.000446  301050.024 0.3
 Stop-CM 5575.000446   55750.004 0.1
 Calc-Ekin   5575.000892  150525.024 0.2
---
 Total  97381137.440   100.0
---
D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

 av. #atoms communicated per step for force:  2 x 94.1

 Average load imbalance: 10.7 %
 Part of the total run time spent waiting due to load imbalance: 0.1 %


 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

 Computing: Nodes Number G-CyclesSeconds %
---
 Domain decomp. 4250  903.835  308.1 1.8
 Comm. coord.   4   1251  321.930  109.7 0.6
 Neighbor search4251 1955.330  666.5 3.8
 Force  4   1251  696.668  237.5 1.4
 Wait + Comm. F 4   1251  384.107  130.9 0.7
 PME mesh   4   125143854.81814948.285.3
 Write traj.4   50011.4890.5 0.0
 Update 4   1251 1137.630  387.8 2.2
 Comm. energies 4   1251 1074.541  366.3 2.1
 Rest   41093.194  372.6 2.1
-