Re: [gmx-users] the mdp file

[Justin A. Lemkul]

He, Yang wrote:

Hi all users,

When I change the value of nsteps in my mdp file to run the gromacs and show 
the trajectory in the gromcas, I found that only the value of nsteps is set by 
10, is there just  the animation of the molecule's movement . I have tried many 
time and set the other values of nsteps, there isn't any movement about the 
molecule at all.



I'm not quite clear on what the problem is.  But you should be aware that 10 
steps (0.02 ps in your case!) is an exceedingly short timeframe under any 
circumstances.


If what you've shown is your full .mdp file, then the other values will be taken 
as default.  For output (nstxout) this value is 100.  So you will likely only 
see the starting and ending coordinates of your 10-step simulation.


Try a longer simulation (>100 steps) or specify nstxout = 1 and see if you 
generate 10 frames.


-Justin


I am strange about that and this is my part of mdp file:

;VARIOUS PREPROCESSING OPTIONS
title= atom
; Preprocessor - specify a full path if necessary.
cpp  = cpp
define   =

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.002
nsteps   = 10
; For exact run continuation or redoing part of a run
init_step= 0
; mode for center of mass motion removal
comm-mode= Linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps=




; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 1
; ns algorithm (simple or grid)c 4
ns_type  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc  = xyz
; nblist cut-off
rlist= 0.686
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = User
rcoulomb-switch  = 0
rcoulomb = 0.9
; Relative dielectric constant for the Cut-off or DC of the reaction field
epsilon-r= 78
; Method for doing Van der Waals
vdw-type = User
; cut-off lengths
rvdw-switch  = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Seperate tables between energy group pairs
energygrp_table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no


Can anyone of you tell me what is the problem?

Thank you very much.

Yang
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--


Justin A. Lemkul
Graduate Research Assistant
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] the mdp file

[He, Yang]

Hi all users,

When I change the value of nsteps in my mdp file to run the gromacs and show 
the trajectory in the gromcas, I found that only the value of nsteps is set by 
10, is there just  the animation of the molecule's movement . I have tried many 
time and set the other values of nsteps, there isn't any movement about the 
molecule at all.

I am strange about that and this is my part of mdp file:

;VARIOUS PREPROCESSING OPTIONS
title= atom
; Preprocessor - specify a full path if necessary.
cpp  = cpp
define   =

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.002
nsteps   = 10
; For exact run continuation or redoing part of a run
init_step= 0
; mode for center of mass motion removal
comm-mode= Linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps=




; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 1
; ns algorithm (simple or grid)c 4
ns_type  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc  = xyz
; nblist cut-off
rlist= 0.686
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = User
rcoulomb-switch  = 0
rcoulomb = 0.9
; Relative dielectric constant for the Cut-off or DC of the reaction field
epsilon-r= 78
; Method for doing Van der Waals
vdw-type = User
; cut-off lengths
rvdw-switch  = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Seperate tables between energy group pairs
energygrp_table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no


Can anyone of you tell me what is the problem?

Thank you very much.

Yang
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Re: [gmx-users] doubt about the ffencadv.rtp

[Mark Abraham]

Serena Leone wrote:

Dear all,

I was trying to model a peptide that I built from scratch with Chimera 
to use in some simulation with Gromacs 4 (encad vacuum ff). After 
moduifying the atom names in the pdb accordingly to rtp for 
ffencadv.rtp, I keep obtaining this error from pdb2gmx:


Program pdb2gmx, VERSION 4.0
Source code file: pgutil.c, line: 87

Fatal error:
Atom H not found in residue 3 while adding improper

Residue 3 in my case is a Pro, and, not being terminal, it is not 
supposed to have an amide H. Now, I know that is usually not recommended 
to play with the ff rtp files, but it seems to me an error in the rtp, 
that maybe needs to be corrected:


rtp entry:

[ PRO ]
[ atoms ]
NN 0.000 0
   CAC1   -0.119 1
   HAH 0.119 1
   CBCP   -0.238 2
  HB1H 0.119 2
  HB2H 0.119 2
   CGCP   -0.238 3
  HG1H 0.119 3
  HG2H 0.119 3
   CDCP   -0.238 4
  HD1H 0.119 4
  HD2H 0.119 4
CAprime0.380 5
OO-0.380 5
[ bonds ]
NCA
   CAHA
   CACB
   CA C
   CB   HB1
   CB   HB2
   CBCG
   CG   HG1
   CG   HG2
   CGCD
   CD   HD1
   CD   HD2
   CD N
C O
   -C N
[ dihedrals ]
  -CA -C  N CD
  -C   N CA  C
   N  CA CB CG
   N  CA  C +N
  CA  CB CG CD
  CB  CG CD  N
[ impropers ]
   -C CA  N  H  improper_X_X_N_X
N  C CA HA  improper_X_X_C_X
N  C CA CB  improper_N_A_C1_C
   CA CG CBHB1  improper_X_X_C_X
   CA CG CBHB2  improper_X_X_C_X
   CB CD CGHG1  improper_X_X_C_X
   CB CD CGHG2  improper_X_X_C_X
   CG  N CDHD1  improper_X_X_C_X
   CG  N CDHD2  improper_X_X_C_X
   -C CD  N CA  improper_X_X_N_X
   CA +N  C  O  improper_X_X_A_X

Now, my guess would be, to describethe same improper, that it should read:

-C CA  N  CD  improper_X_X_N_X

instead of

-C CA  N  H  improper_X_X_N_X

am I right, or am I overlooking something?


I don't know anything about this force field, but the line under 
discussion was not present in 3.3.x versions of GROMACS. Improper 
dihedrals are used to help enforce planarity of four atoms. As such, 
only two are required to keep -CA, -C, -O, N, H, CA moiety coplanar 
given the existence of a -CA, -C, N, C normal dihedral. All the other 
peptide linkages have only the two impropers as indicated in the last 
two lines of [impropers] for PRO above. Thus, I think this proline 
residue topology got broken in the source distribution between the 3.3.1 
 version I'm looking at, and 4.0.


Mark
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[gmx-users] doubt about the ffencadv.rtp

[Serena Leone]

Dear all,

I was trying to model a peptide that I built from scratch with Chimera 
to use in some simulation with Gromacs 4 (encad vacuum ff). After 
moduifying the atom names in the pdb accordingly to rtp for 
ffencadv.rtp, I keep obtaining this error from pdb2gmx:


Program pdb2gmx, VERSION 4.0
Source code file: pgutil.c, line: 87

Fatal error:
Atom H not found in residue 3 while adding improper

Residue 3 in my case is a Pro, and, not being terminal, it is not 
supposed to have an amide H. Now, I know that is usually not 
recommended to play with the ff rtp files, but it seems to me an error 
in the rtp, that maybe needs to be corrected:


rtp entry:

[ PRO ]
[ atoms ]
NN 0.000 0
   CAC1   -0.119 1
   HAH 0.119 1
   CBCP   -0.238 2
  HB1H 0.119 2
  HB2H 0.119 2
   CGCP   -0.238 3
  HG1H 0.119 3
  HG2H 0.119 3
   CDCP   -0.238 4
  HD1H 0.119 4
  HD2H 0.119 4
CAprime0.380 5
OO-0.380 5
[ bonds ]
NCA
   CAHA
   CACB
   CA C
   CB   HB1
   CB   HB2
   CBCG
   CG   HG1
   CG   HG2
   CGCD
   CD   HD1
   CD   HD2
   CD N
C O
   -C N
[ dihedrals ]
  -CA -C  N CD
  -C   N CA  C
   N  CA CB CG
   N  CA  C +N
  CA  CB CG CD
  CB  CG CD  N
[ impropers ]
   -C CA  N  H  improper_X_X_N_X
N  C CA HA  improper_X_X_C_X
N  C CA CB  improper_N_A_C1_C
   CA CG CBHB1  improper_X_X_C_X
   CA CG CBHB2  improper_X_X_C_X
   CB CD CGHG1  improper_X_X_C_X
   CB CD CGHG2  improper_X_X_C_X
   CG  N CDHD1  improper_X_X_C_X
   CG  N CDHD2  improper_X_X_C_X
   -C CD  N CA  improper_X_X_N_X
   CA +N  C  O  improper_X_X_A_X

Now, my guess would be, to describethe same improper, that it should read:

-C CA  N  CD  improper_X_X_N_X

instead of

-C CA  N  H  improper_X_X_N_X

am I right, or am I overlooking something?

Thank you very much,
Cheers,
Serena
--

Serena Leone, Ph.D.
Brigham and Women's Hospital
Harvard Medical School
Channing Laboratory EBRC 609
221 Longwood Avenue
Boston, MA 02115
(tel)  617-732-8586






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Re: [gmx-users] running a simulation without production

[Mark Abraham]

Zuzana Benkova wrote:
I have tried also running this job without user specified potential, 
with relaxed plate, with pbc=no and some other attempts, but I always 
failed in the same way. I would be very thankful for suggestions how to 
cope with this problem.


Do other simulations run? Try one of the tutorials or gmxtest.pl.

Mark
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Re: [gmx-users] gromacs-4: statring in parallel on solaris 8

[Roland Schulz]

You can run on many processors with MPI.

Only threads are not supported. Threads were also not supported in 3.

Threads are light weight shared memory processes and thus different from MPI
processes.

You can use MPI in all practical cases.

On Mon, Nov 3, 2008 at 12:11 PM, DimitryASuplatov <[EMAIL PROTECTED]> wrote:

>
> >
> > The is no multi-threading in 4.0.
> >
> > Berk
> >
>
> ?!
> What do you mean "there is no multi-threading in 4.0" ? May be I have
> incorrectly defined "multithreading", but if gromacs-4 does not yet
> support running on multiple processors then I realy do not understand
> why is it released as final version?
>
> Thank you for your answers.
> SDA
>
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-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
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Re: [gmx-users] question about default parameter for g_hbond

[Xavier Periole]

On Mon, 3 Nov 2008 17:59:33 +0100
 Thomas Schlesier <[EMAIL PROTECTED]> wrote:

Hi all,
does somebody know from where the default parameters for g_hbond (angle
Acceptor-Hydrogen-Donor = 30° ; distance Acceptor-Donor = 0.35nm) are?
I found nothing in the manual about that.

If you type g_hbond -h the default values are indicated.


Thomas
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-
XAvier Periole - PhD

- Molecular Dynamics Group -
NMR and Computation
University of Groningen
The Netherlands
-
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RE: [gmx-users] gromacs-4: statring in parallel on solaris 8

[DimitryASuplatov]

> 
> The is no multi-threading in 4.0.
> 
> Berk
> 

?!
What do you mean "there is no multi-threading in 4.0" ? May be I have
incorrectly defined "multithreading", but if gromacs-4 does not yet
support running on multiple processors then I realy do not understand
why is it released as final version?

Thank you for your answers.
SDA

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[gmx-users] running a simulation without production

[Zuzana Benkova]

Dear GROMACS users,

 

I want to simulate a system consisting of a plate modeled by atoms (5000
atoms) and a polyethylene chain (80 carbons). The plate is frozen and I am
using tabulated potentials. In this system, the considered interactions are
chain-chain and chain-plate. There are no electrostatic interactions. The
system is placed in a box, with dimensions corresponding to the dimensions
of plate and substantially larger height. My md.mdp file is as follows

 

cpp =  cpp

define  =

 

integrator  =  md

dt  =  0.002

nsteps  =  7500

nstcomm =  1

comm_mode   =  None

nstxout =  10

nstvout =  10

nstfout =  10

nstxtcout   =  10

nstlog  =  10

nstenergy   =  10

energygrps  =  Chain Plate

freezegrps  =  Plate

freezedim   =  Y Y Y

energygrp_excl  =  Plate Plate

energygrp_table =  Chain Chain Chain Plate

nstlist =  1

ns_type =  simple

rlist   =  0.4

pbc =  xyz

vdw-type=  User

rvdw=  0.4

coulombtype =  cut-off

rcoulomb=  0.1

Tcoupl  =  nose-hoover

tc-grps =  System

tau_t   =  0.1

ref_t   =  450

gen_vel =  yes

gen_temp=  450

constraints =  none

pcoupl  =  no

 

After launching this job the process is running but there is no trajectory
to be produced. The log file finishes in the section containing following
information

 

   energygrp_flags[  0]: 2 2

   energygrp_flags[  1]: 2 1

 

I have tried also running this job without user specified potential, with
relaxed plate, with pbc=no and some other attempts, but I always failed in
the same way. I would be very thankful for suggestions how to cope with this
problem. 

 

Greetings

 

Zuzana

 

 

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[gmx-users] question about default parameter for g_hbond

[Thomas Schlesier]

Hi all,
does somebody know from where the default parameters for g_hbond (angle
Acceptor-Hydrogen-Donor = 30° ; distance Acceptor-Donor = 0.35nm) are?
I found nothing in the manual about that.

Thomas
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RE: [gmx-users] periodic boundary conditions in g_rdf

[ilhan favela]

Hi Berk, thanks for the answearing.

Here is my command line:

g_rdf -f file.xtc -s file.tpr -n index.ndx -com -rdf mol_com -xy

then i select 'Protein' as reference group and 'upper-leaf_&_P8' (just the P8 
atoms from the upper-leaflet) in the 1 group option.

The value of the g_rdf at the half of the box is roughly 0.5 - 0.6

In the attachment is de g(r) that i got.

Thanks in advance!
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] periodic boundary conditions in g_rdf
Date: Mon, 3 Nov 2008 10:20:08 +0100

Hi,

To what value does your rdf go then?

You have pbc in your system, so running with -nopbc is incorrect.
The rdf will then stop at half the box, since you molecules are in the box
and your peptide is probably in the middle, leading to a longest distance
of roughly half the box.

Berk



From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Date: Fri, 31 Oct 2008 16:55:54 -0600
Subject: [gmx-users] periodic boundary conditions in g_rdf


Hi everybody.
I'm working a system with a peptide embedded in a lipid bilayer and I try to 
get the two-dimentional g_rdf for the upper leaflet around the peptide with the 
-xy option and periodic boundary conditions. But my RDF doesn't go to 1. When a 
used -nopbc i get almost the same result (just multiplied by a constant) and 
the RDF is always cutted at the half of size of the box.

Any help will be appreciated.

Thanks in advance.


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RE: [gmx-users] Problems of test particle insertion with gromacs 4.0

[Berk Hess]

Hi,

I should remove the warning of cut-off with TPI.
It would be nice if you could use PME, but that requires a lot of coding.
Note that you should probably use quite a long cut-off.

The result indeed depends on nsteps, as you should expect.
nsteps should be so large that your results converge.
But for convergence it is also required that you have enough sampling
of your original system in and over all your frames.

Berk

Date: Mon, 3 Nov 2008 22:37:57 +0800
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] Problems of test particle insertion with gromacs 4.0

Hi all,
   I'm trying to use gromacs 4.0 to carried out some calculations with test 
particle insertion algorithm. 
   Here are my operations:
   0. Carried out a common NPT simulation with N molecules, I got the .trr file;
   1. prepare .top and .gro with N+1 molecules (including the test particle);
   2. use grompp to get the .tpr for mdrun;
   3. mdrun -rerun .trr.
   In this way, I finally got two files tpi.xvg and tpidist.xvg. The procedure 
seems fine, isn't it?
   Nevertheless, I have some problems here:
   1. when I was trying to use pme (or EWALD) for the electrostatics, the 
grompp stopped with an error: "TPI does not work with full electrostatics". But 
if I use cut-off, the grompp works but generates a warning to recommend the use 
of pme or reaction field. What's wrong here?

   2. The final output of mu seems to be sensitive to the choice of nsteps 
(I've tried from 1000 to 1). How to choose an appropriate one?
 
Thanks for your possible suggestions!
 
zgzhang

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RE: [gmx-users] gromacs-4: statring in parallel on solaris 8

[Berk Hess]

> Date: Mon, 3 Nov 2008 10:33:41 -0500
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] gromacs-4: statring in parallel on solaris 8
> 
> 
> 
> DimitryASuplatov wrote:
> > Hello,
> > I have installed gromacs-4 on Solaris 8 with mpi support.
> > I was very disappointed by the lack of -np option in grompp and mdrun.
> 
> The -np option is absent in grompp, as it is no longer necessary.  The -np 
> flag 
> is indeed present for mdrun, however.

The mdrun flag has been removed from mdrun a long time ago,
it was already gone in 3.3 (but mdrun does not check for incorrect
command line options).

> 
> > After reading the manual and the site I came to a conclusion that now we
> > do not need to specify number of nodes via gromacs status file but
> > instead use mpirun option only.
> > Executing (for gromacs benchmarking set)
> > 
> > grompp
> > mpirun c0-5 mdrun_mpi -v
> > 
> > starts six threads on six processors though output speed is the same as
> > for a single-node run. No errors, no warnings.
> >
> 
> I didn't think threading was supported yet, maybe I'm wrong.  But you can 
> definitely use -np 6 with mdrun_mpi.

The is no multi-threading in 4.0.

Berk


> 
> -Justin
> 
> 
> > So, am I doing wrong with gromacs parallelization or is this the problem
> > of the Solaris MPI?
> > 
> > Thank you.
> > 
> > 
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
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> > 
> 
> -- 
> 
> 
> Justin A. Lemkul
> Graduate Research Assistant
> 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] partial charges, editconf -grasp

[Justin A. Lemkul]

Una Bjarnadottir wrote:

Dear Gromacs users,

I want to extract partial charges from a trajectory file. I know only of
using trjconv to write individual frames to individual files and then using
editconf with the grasp option on each of these files. But when I do:

editconf -f xxx.gro -o xxx.pdb -grasp

I get the following error:

Fatal error:
Input file should be a .tp[abr] file when using the -mead option.

I thought this was a version 3.3.x problem after reading "Editconf fix" on
http://www.gromacs.org/pipermail/gmx-revision/2008-February/000202.html. 
But

I just upgraded to version 4.0 and I get the exact same error. Can anyone
help me with this problem? Is there perhaps an easier way of getting the
partial charges?



Have you done what editconf is telling you?  Charges are not stored in 
coordinate files by default, so there are no charges to read.  Charges are, 
however, in the topology (.top), which is then passed to the .tpr file.  If you 
supply the .tpr, it should work.


-Justin


Kind regards,
Una



--


Justin A. Lemkul
Graduate Research Assistant
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] gromacs-4: statring in parallel on solaris 8

[Justin A. Lemkul]

DimitryASuplatov wrote:

Hello,
I have installed gromacs-4 on Solaris 8 with mpi support.
I was very disappointed by the lack of -np option in grompp and mdrun.


The -np option is absent in grompp, as it is no longer necessary.  The -np flag 
is indeed present for mdrun, however.



After reading the manual and the site I came to a conclusion that now we
do not need to specify number of nodes via gromacs status file but
instead use mpirun option only.
Executing (for gromacs benchmarking set)

grompp
mpirun c0-5 mdrun_mpi -v

starts six threads on six processors though output speed is the same as
for a single-node run. No errors, no warnings.



I didn't think threading was supported yet, maybe I'm wrong.  But you can 
definitely use -np 6 with mdrun_mpi.


-Justin



So, am I doing wrong with gromacs parallelization or is this the problem
of the Solaris MPI?

Thank you.


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--


Justin A. Lemkul
Graduate Research Assistant
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] gromacs-4: statring in parallel on solaris 8

[DimitryASuplatov]

Hello,
I have installed gromacs-4 on Solaris 8 with mpi support.
I was very disappointed by the lack of -np option in grompp and mdrun.
After reading the manual and the site I came to a conclusion that now we
do not need to specify number of nodes via gromacs status file but
instead use mpirun option only.
Executing (for gromacs benchmarking set)

grompp
mpirun c0-5 mdrun_mpi -v

starts six threads on six processors though output speed is the same as
for a single-node run. No errors, no warnings.

So, am I doing wrong with gromacs parallelization or is this the problem
of the Solaris MPI?

Thank you.


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[gmx-users] partial charges, editconf -grasp

[Una Bjarnadottir]

Dear Gromacs users,

I want to extract partial charges from a trajectory file. I know only of
using trjconv to write individual frames to individual files and then using
editconf with the grasp option on each of these files. But when I do:

editconf -f xxx.gro -o xxx.pdb -grasp

I get the following error:

Fatal error:
Input file should be a .tp[abr] file when using the -mead option.

I thought this was a version 3.3.x problem after reading "Editconf fix" on
http://www.gromacs.org/pipermail/gmx-revision/2008-February/000202.html. But
I just upgraded to version 4.0 and I get the exact same error. Can anyone
help me with this problem? Is there perhaps an easier way of getting the
partial charges?

Kind regards,
Una

--
Una Bjarnadottir   School of Biomolecular and Biomedical Science
Conway Institute   UCD
Dublin 4, Ireland  Phone: +353 1 716 6874, Fax: +353 1 716 6898
Email: [EMAIL PROTECTED] 


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Re: [gmx-users] g_potential

[Justin A. Lemkul]

minnale wrote:
 
Hi,
I have small doubt that when we calculate elctrostaic potenitial of 
POPC  ,get system with neutral, POPC positive and water negative values,
what is the reason behind that POPC has positive and water has negative 
values.


I'm not terribly familiar with g_potential, but in terms of thermodynamics, 
potential energy can be either positive or negative.


water has H+ ion and OH- ion it should be neutral but why negative 
values it showing.




Do you actually have explicit H+ and OH- ions in your system?  If you do, I'd be 
interested in the parameters you used, because AFAIK these species are not 
parameterized for use with most common force fields.


In reality, these species are present in water, but it still has no real bearing 
on whether or not the electrostatic potential should be inherently positive or 
negative.


-Justin


Any suggestions would be appreciated.

Thanks in advance.



Rediff Shopping 






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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_potential

[minnale]

  
Hi,
I have small doubt that when we calculate elctrostaic potenitial of POPC  ,get 
system with neutral, POPC positive and water negative values, 
what is the reason behind that POPC has positive and water has negative values.
water has H+ ion and OH- ion it should be neutral but why negative values it 
showing.

Any suggestions would be appreciated. 

Thanks in advance.___
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[gmx-users] Problems of test particle insertion with gromacs 4.0

[Zhang Zhigang]

Hi all,
   I'm trying to use gromacs 4.0 to carried out some calculations with test
particle insertion algorithm.
   Here are my operations:
   0. Carried out a common NPT simulation with N molecules, I got the .trr
file;
   1. prepare .top and .gro with N+1 molecules (including the test
particle);
   2. use grompp to get the .tpr for mdrun;
   3. mdrun -rerun .trr.
   In this way, I finally got two files tpi.xvg and tpidist.xvg. The
procedure seems fine, isn't it?
   Nevertheless, I have some problems here:
   1. when I was trying to use pme (or EWALD) for the electrostatics, the
grompp stopped with an error: "TPI does not work with full electrostatics".
But if I use cut-off, the grompp works but generates a warning to recommend
the use of pme or reaction field. What's wrong here?
   2. The final output of mu seems to be sensitive to the choice of nsteps
(I've tried from 1000 to 1). How to choose an appropriate one?

Thanks for your possible suggestions!

zgzhang
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Sv: Re: [gmx-users] surface simulation

[Peter Ahlström]

If vapour pressure is not too high, I think it is physically more
relevant to simulate a CCl_4
slab with periodic boundary conditions suck that you get an infinite
2-slab repeated in the third 
dimension such that you get a vapour slab in between (surface tensions
etc are normally 
measured in equilibrium with the vapour). So, in my opinion, the easiest
thing to do is to simulate 
a slab of CCl_4 together with the vapour (at least you get less
artefacts from bad wall models
in that way). At least that is a somewhat physical system. Normally I do
not think that position
restraints are needed (but I have no experience with CCl_4)

Cheers,
Peter


Dr. Peter Ahlström
School of Engineering
University of Borås 
SE-501 90 Borås
Ph. +46-33-435 46 75 Fax +46-33-435 40 08
[EMAIL PROTECTED]
>>> Mark Abraham <[EMAIL PROTECTED]> 08-11-03 05:08 >>>
Hongyan Xiao wrote:
> Hi, Mark Abraham,
>  
> I accepted your suggestion on the language.
>  
> I simulated the CCl_4 surface system. In order to simplify model,
using 
> the vacuum replaced the gas phase. Furthermore, I found some paper by 
> other people also deal with the gas/liquid using the vacuum. In 
> vacuum/CCl_4 , can I control the CCl_4 molecule not to run to the
vacuum 
> using the gromacs? For example, using the wall, but I do not set up
wall 
> parameters well. Please give me some suggestion. Thanks again!

Some position restraints will keep your surface intact. See the manual 
for details. GROMACS will report how much "energy" is going from the 
restraints and you should check your parameterization by seeing that 
this energy is pretty small.

Mark
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Re: [gmx-users] about PMF calculation

[Xavier Periole]

On Mon, 3 Nov 2008 05:25:38 -0800 (PST)
 chiloo Laohpongspaisan <[EMAIL PROTECTED]> wrote:

Dear all,

 

I'd like to ask about the calculation of potential of mean force.

Is it possible to calculate PMF from trajectory? Or do we need to apply 
"pull code" or "free energy code" before MD running?

If you have complete sampling you can get the PMF from the histogram
along your reaction coordinate.


 

Regards,

Chiloo

 Other Mails:
[EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED] 



 


-
XAvier Periole - PhD

- Molecular Dynamics Group -
NMR and Computation
University of Groningen
The Netherlands
-
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[gmx-users] about PMF calculation

[chiloo Laohpongspaisan]

Dear all,

 

I'd like to ask about the calculation of potential of mean force.

Is it possible to calculate PMF from trajectory? Or do we need to apply "pull 
code" or "free energy code" before MD running?

 

Regards,

Chiloo

 Other Mails:
[EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED] 


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[gmx-users] GROMOS [BMIM][PF6] and [BMIM][NO3] Ionic liquid force field

[Nuno Micaelo]

Dear Naimah Haron Naimah
If you are interested in Ionic Liquid force fields, see the paper:
Title: Parametrization of 1-butyl-3-methylimidazolium
hexafluorophosphate/nitrate ionic liquid for the GROMOS force field
Author(s): Micaelo, NM; Baptista, AM; Soares, CM
Source: JOURNAL OF PHYSICAL CHEMISTRY B   Volume: 110   Issue: 29
Pages: 1-14451   Published: JUL 27 2006
and for the recent study of proteins in Ionic Liquids, see:

Title: Protein structure and dynamics in ionic liquids. Insights from
molecular dynamics simulation studies
Author(s): Micaelo, NM; Soares, CM
Source: JOURNAL OF PHYSICAL CHEMISTRY B   Volume: 112   Issue: 9
Pages: 2566-2572   Published: 2008

I will put these parameters in the User Contribution area in gromacs
website, in the mean time you can e-mail
me.

-- 
Nuno Micaêlo, PhD
[EMAIL PROTECTED]

Molecular Modelling Group
ESSUA - Universidade de Aveiro
Campus Universitário de Santiago
3810-193, Aveiro
PORTUGAL

www.nunomicaelo.com
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Re: [gmx-users] Fwd: still problem with lamboot

[Carsten Kutzner]

So for the two cores on your notebook it works?

If you can get an answer from the remote host by using
e.g. "ping remotehost" then lamboot should in principle
also work. If it does not, carefully read the error message
that comes from lam. It could be that there is some output
on stderr coming from the remote host that lam does not like.

Carsten


sarbani chattopadhyay wrote:
>  
> 
> 
> Note: Forwarded message attached
> 
> -- Original Message --
> 
> From: "sarbani chattopadhyay" <[EMAIL PROTECTED]>
> To: "gmx_usrs" <[EMAIL PROTECTED]>
> Subject: still problem with lamboot
> 
> 
> 
> Rediff Shopping
>   PROTECTED]/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null>
> 
> 
> 
> 
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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-- 
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
www.mpibpc.mpg.de/home/grubmueller/
www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne/
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[gmx-users] Fwd: still problem with lamboot

[sarbani chattopadhyay]

  


Note: Forwarded message attached

-- Original Message --

From: "sarbani chattopadhyay" <[EMAIL PROTECTED]>
To: "gmx_usrs" <[EMAIL PROTECTED]>
Subject: still problem with lamboot
--- Begin Message ---
  Dear  Carsten,
   Thanks for your reply. As per your suggestion I tried to 
create a "lamhost" file 
as

mac-pros-computer.local  cpu=2
remotehostcpu=2

However the lamboot can't figure out the "remotehost" . 
"mac-pros-computer.local" is the 
name of the local host. I can't figure out how to do this corectly. I may have 
a wrong 
conception but I need help regarding this.

Thanks in advance
Sarbani
--- End Message ---
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RE: [gmx-users] periodic boundary conditions in g_rdf

[Berk Hess]

Hi,

To what value does your rdf go then?

You have pbc in your system, so running with -nopbc is incorrect.
The rdf will then stop at half the box, since you molecules are in the box
and your peptide is probably in the middle, leading to a longest distance
of roughly half the box.

Berk



From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Date: Fri, 31 Oct 2008 16:55:54 -0600
Subject: [gmx-users] periodic boundary conditions in g_rdf













Hi everybody.
I'm working a system with a peptide embedded in a lipid bilayer and I try to 
get the two-dimentional g_rdf for the upper leaflet around the peptide with the 
-xy option and periodic boundary conditions. But my RDF doesn't go to 1. When a 
used -nopbc i get almost the same result (just multiplied by a constant) and 
the RDF is always cutted at the half of size of the box.

Any help will be appreciated.

Thanks in advance.



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Re: [gmx-users] problem with lamboot

[Carsten Kutzner]

Hi,

if you just want to use both cores on your local machine, then you do
not necessarily need a hostfile. Just type "lamboot" and later specify
the number of cores you want to use with

mpirun -np 2 mdrun ...

BTW, the hostfile you cite below is not the one LAM expects. Use a simple
text editor to create, say "lamhost", and give the name of each machine
with the number of cores, e.g.

mycomputer cpu=2
remotecomputer cpu=4

This you can use with "lamboot -v lamhost".

Carsten


sarbani chattopadhyay wrote:
>   Hi everybody,
>   I have question regarding parallel run. I am new
> to this and may sound very
> stupid so please bear with me.
> 
>   Our's is a 10.4.1 Mac Os X with 2 X 2.66 GHz Dual -Core Intel
> Xeon processor.
> Gromacs 3.3.1 was loaded in it. Then I had downloaded the "lam-7.06"
> package from the
> gromacs homepage.
> The host file is present in /private/etc/ directory as expected and reads
> ##
> # Host Database
> #
> # localhost is used to configure the loopback interface
> # when the system is booting.  Do not change this entry.
> ##
> 127.0.0.1  localhost
> 255.255.255.255 broadcasthost
> ::1localhost
> 
> 
> 
> However  "lamboot" gives error on running on this host file. I want to
> know the correct way
> to modify the host file so that I can launch the "lam/mpi" environment.
> 
> 
> Any suggestion is welcome.
> 
> Thanks in advance
> Sarbani 
> 
> 
> 
> Rediff Shopping
>   PROTECTED]/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null>
> 
> 
> 
> 
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-- 
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
www.mpibpc.mpg.de/home/grubmueller/
www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne/
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