[gmx-users] any method to determine gaussian curvature of phase

[Sanku M]

Hi,

  I wanted to numerically determine the gaussian curvature of a phase obtained 
by self-assembly of surfactants.
I was wondering whether any one can suggest any tool or any program which can 
create a 3D grid and then calculate the gaussian curvature on points on the 3D 
grid .

Thanks

Sanku-- 
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[gmx-users] Number of native contacts rho

[Sanku M]

Hi,
  Is there any tool in gromacs that can compute the fraction of native contacts 
 rho ( i,e  the typical parameter that quantifies how close the folding 
protein is to the native ) ?
Thanks
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[gmx-users] problem with plumed version of gromacs in replica exchange

[Sanku M]

Dear Users ,

  I am trying to use PLUMED with gromacs4.5.4 to perform umbrella sampling 
simulation using replica exchange as implemented within gromacs. I am using 
radius of gyration as the collective variable along which umbrella sampling is 
being performed. However, I find that whenever I try to run replica exchange 
with umbrella sampling using the plumed compiled gromacs, it always crashes 
saying that 

 The properties of the 23 systems are all the same, there is nothing to 
exchange
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors;

I had generated 23 replica each corresponding to a particular temperature and 
then used grompp (compiled using plumed ) to generate 23 .tpr file. Now, I use 
only one plumed.dat file . But, running the simulation using command

~/UTIL/OPENMPI/bin/mpirun -np 46  mdrun_plumed_s -multi 23 -replex 500 -s hremd 
-plumed plumed_umb.dat  log_replica

But, it ctashes..

I have also tried running regular replica exchange simulation without this 
plumed.dat file and then again it crashes saying the same error that it finds 
all replica identical.

However, same simulation with official gromacs 4.5.4 executable ( i.e without 
the plumed plugin) runs without any problem. 
Also, the plumed plugin works great for a single temperature simulation.

So, I wonder whether the plumed plugin is causing any trouble in running 
replica exchange simulation or I am missing something.
Thanks in advance for help
Sanku -- 
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[gmx-users] query on table potential

[Sanku M]

Hi,
  I am trying to use a table potential implementing Weeks-Chandler-Anderson 
(WCA) interaction between a solute and all atoms of a solvent like TIP3P water 
( with nonzero interaction in the Hydrogen atoms) . But, I am having a trouble 
in specifying energy groups required for table potential. 
Here is the problem:
 I have two atom types in water : OW and HW. and one atom type in solute : POL

Now, I want to use  two Table potentials with WCA interactions between a) POL  
HW and b) POL  OW 
So, I created two table potential files: table_POL_HW.xvg and table_POL_OW.xvg

and then
in the .mdp file, I specified 
energygrps = POL OW HW 
energygrps_table = POL OW POL HW

But, compiling the .mdp file using grompp ( version 4.5.4)  gives me following 
error
Fatal error:                
atoms 33 and 34 in charge group 1 of molecule type 'SOL' are in different 
energy groups

Clearly, using OW and HW as separate energy groups is causing the problem.
So, I am looking for an option on how I can use the table potential between 
solute and each atoms of solvent.

Any help will be appreciated.
Sanku-- 
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[gmx-users] problem with pull code

[Sanku M]

Hi all,
  I am trying to do an umbrella sampling of a fairly extended state of the 
protein along end-to-end distance of it. I am using a rectangular box ( 
elongated along x ) of dimension 20 nm X 8nm X 8 nm. I am doing the simulation 
in NVT ensemble. gromacs 4.5.4 is being used.

But, even after running for 1 ns, the simulation crashes saying that 

Program mdrun_5mpi, VERSION 4.5.4
Source code file: pull.c, line: 329

Fatal error:
Distance of pull group 1 (2.940209 nm) is larger than 0.49 times the box size 
(9.00)


But if I see the trajectory, it hardly shows any issue with seeing the PBC 
image . I am not sure how to avoid this issue.
Should I make one of the endgroup as freeze group so that it does not get 
tilted.
Any help will be appreciated.
Sanku
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[gmx-users] Using umbrella sampling at constant force

[Sanku M]

Hi,
  I am trying to compute free energy of a polymer in presence of a constant 
force.
If I understand correctly, I need to use two pull-option here in gromacs: one 
for performing umbrella sampling and other for applying  constant force. But, 
as far as I know I can not specify two pull option in single mdp file of 
gromacs. 
So, I was wondering whether there is any way out in gromacs regarding this 
issue.
Thanks
Sanku
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[gmx-users] carbohydrate forcefield in gromacs

[Sanku M]

Hi,
  Is carbohydrate forcefield in Charmm or Amber included in gromacs4.5.5 
topology folders ? 
Sanku
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Re: [gmx-users] fraction of native contacts calculation

[Sanku M]

Bipin,
  There might be a workaround. You might want to check out Plumed plugin in 
latest versions of VMD for calculating fractions of native contact. You can 
load the gromacs trajectory along with the native .gro file in VMD and use 
Plumed plugin inbuilt in VMD . You need to install plumed most probably early.




 From: bipin singh bipinel...@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org 
Sent: Thursday, November 1, 2012 1:23 PM
Subject: Re: [gmx-users] fraction of native contacts calculation
 
Thanks for your response. Hope to see this feature in upcoming GROMACS
release. Before that, could it be possible to get the modified code in the
user contribution section, it may be useful for many GROMACS users.


On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund er...@xray.bmc.uu.se wrote:


 31 okt 2012 kl. 13.43 skrev Justin Lemkul:

 
 
  On 10/31/12 6:02 AM, bipin singh wrote:
  Hello all,
 
  Is there any way to calculate fraction of native contacts during the
  simulation in gromacs. I searched the archives but didn't found any
  significant clue.
 
  At present, there is no way to do this.  Likely one could modify the
 g_mindist code to do this - it would be a very nice feature.
 

 If one could get the -sel option of g_hbond to work again then you would
 get such information with -contact.

 Erik


  -Justin
 
  --
  
 
  Justin A. Lemkul, Ph.D.
  Research Scientist
  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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 ---
 Erik Marklund, PhD
 Dept. of Cell and Molecular Biology, Uppsala University.
 Husargatan 3, Box 596,    75124 Uppsala, Sweden
 phone:    +46 18 471 6688        fax: +46 18 511 755
 er...@xray.bmc.uu.se
 http://www2.icm.uu.se/molbio/elflab/index.html

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-- 
---
*Regards,*
Bipin Singh
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[gmx-users] g_bar and second law violations

[Sanku M]

Hi,
  I am trying to compute the free energy change using g_bar: I am using 
two-stage decoupling process as in Justin Lemkul's tutorial.
But , I get following warning in all cases regarding violation of second law of 
thermodynamics. Can someone explain what is this error about and which lambda I 
should look for?
Here is the output.

 Detailed results in kT (see help for explanation):

 lam_A  lam_B      DG   +/-     s_A   +/-     s_B   +/-   stdev   +/- 
 0.000  0.100   -0.39  0.08   -0.64  0.06   -0.09  0.20    0.88  0.05
 0.100  0.150    0.08  0.04    0.07  0.03    0.09  0.05    0.43  0.01
 0.150  0.200    0.12  0.02   -0.11  0.03    0.36  0.06    0.54  0.02
 0.200  0.300    0.54  0.06   -0.05  0.07    1.25  0.15    1.24  0.03
 0.300  0.350    0.21  0.03    0.15  0.04    0.31  0.06    0.72  0.01
 0.350  0.400   -0.01  0.02    0.11  0.03   -0.08  0.04    0.64  0.01
 0.400  0.500   -0.37  0.03    0.22  0.02   -0.78  0.06    1.07  0.01
 0.500  0.600   -0.58  0.01    0.17  0.04   -1.17  0.04    0.99  0.01
 0.600  0.700   -0.74  0.03    0.16  0.02   -1.51  0.07    0.89  0.01
 0.700  0.750   -0.37  0.01   -0.02  0.02   -0.69  0.03    0.47  0.01
 0.750  0.800   -0.26  0.01   -0.07  0.01   -0.42  0.02    0.53  0.01
 0.800  0.850   -0.19  0.01    0.03  0.01   -0.38  0.03    0.57  0.01
 0.850  0.900   -0.24  0.02    0.06  0.01   -0.50  0.04    0.58  0.01
 0.900  1.000   -0.47  0.07   -0.04  0.05   -0.12  0.34    1.13  0.06

WARNING: Some of these results violate the Second Law of Thermodynamics: 
         This is can be the result of severe undersampling, or (more likely)
         there is something wrong with the simulations.


Final results in kJ/mol:

lambda  0.000 -  0.100,   DG -0.97 +/-  0.19
lambda  0.100 -  0.150,   DG  0.20 +/-  0.09
lambda  0.150 -  0.200,   DG  0.30 +/-  0.05
lambda  0.200 -  0.300,   DG  1.34 +/-  0.15
lambda  0.300 -  0.350,   DG  0.52 +/-  0.07
lambda  0.350 -  0.400,   DG -0.02 +/-  0.05
lambda  0.400 -  0.500,   DG -0.92 +/-  0.08
lambda  0.500 -  0.600,   DG -1.45 +/-  0.03
lambda  0.600 -  0.700,   DG -1.86 +/-  0.08
lambda  0.700 -  0.750,   DG -0.91 +/-  0.03
lambda  0.750 -  0.800,   DG -0.64 +/-  0.03
lambda  0.800 -  0.850,   DG -0.48 +/-  0.03
lambda  0.850 -  0.900,   DG -0.61 +/-  0.04
lambda  0.900 -  1.000,   DG -1.17 +/-  0.18

total   0.000 -  1.000,   DG -6.68 +/-  0.30
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[gmx-users] simulating protein in gas-phase

[Sanku M]

Dear Gromacs users,
  I am trying to perform a MD simulation in gromacs 4.5.4 using a protein and 
ligand in gas phase.
I have previously run the simulation in water without any problem. Now, I want 
to compare the result to see the effect of solvent.

But for running the same simulation after stripping the waters from the 
simulation box I am looking for some advise.
I am having following issues:
a) If I use 'md' i.e usual leap frog integrator with nstcomm=10 and 
comm-mode=Linear( this was the setup I had when I ran the simulation in water), 
I find after running the system of protein and ligand in gas phase for some 
time ( about 1 ns ), the protein starts rotating i.e it generates a very high 
angular momentum.
b) So, I thought of using comm-mode=angular,,, But then grompp gives me a 
warning that removing rotation is not a problem only if I have only 1 molecule 
in the system ...which is not the case here as I have ligand and some ions . 
Any suggestion is highly appreciated. I can change nstcomm=1 using 
comm-mode=Linear but I am not sure it will stop the rotation of the protein 
about its own axis.
I am running the system using periodic boundary condition and using PME for 
electrostatics.

c) another option I thought of was using 'sd' integrator but considering my 
simulation in water having been performed using md integrator, I was looking to 
keep my .mdp file option as similar as possible in both cases.

Any help on how to perform the simulations in gas-phase will be highly 
appreciated.

Here is my current .mdp options:
title       = Umbrella pulling simulation
; Run parameters
integrator  = md
dt          = 0.002
tinit       = 0
nsteps      = 150     ; 800 ps
nstcomm     = 10
; Output parameters
nstxout     =       ; every 10 ps
nstvout     = 
nstfout     = 
nstxtcout   = 250
nstenergy   = 250
; Bond parameters
constraint_algorithm    = lincs
constraints             = hbonds
continuation            = yes
; Single-range cutoff scheme
nstlist     = 5
ns_type     = grid
rlist       = 1.4
rcoulomb    = 1.4
rvdw        = 1.4
; PME electrostatics parameters
coulombtype     = PME
fourierspacing  = 0.12
fourier_nx      = 0
fourier_ny      = 0
fourier_nz      = 0
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes
; Berendsen temperature coupling is on in two groups
Tcoupl      = Nose-Hoover
tc_grps     =  System
tau_t       = 0.5
ref_t       = 300
; Pressure coupling is on
Pcoupl          = no
pcoupltype      = isotropic
tau_p           = 1.0
compressibility = 4.5e-5
ref_p           = 1.0
; Generate velocities is on
gen_vel     =  yes
; Periodic boundary conditions are on in all directions
pbc     = xyz
; Long-range dispersion correction
DispCorr    = EnerPres

Thanks
Sanku
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[gmx-users] mdp option for implicit solvent simulation

[Sanku M]

Hi,
  I am trying to do implicit solvent simulation for a protein in gas-phase. I 
have a few questions :
1) should I use sd integrator?

2) should I also use no periodic condition considering continuum dielectric ?

3) in the JCTC 2010 paper by Lindahl and co-worker, it is mentioned that no 
cutoffs were used for implicit solvent simulations. 
 But, again in implicit solvent setup the rgblist should be equal to rlist.
Now, if I use rlist=0 ( as all interactions are considered), should I also make 
rgblist=0?
Does it mean the setup was following type: i.e.
 
  ; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 0
; ns algorithm (simple or grid)
ns-type                  = simple
; Periodic boundary conditions: xyz, no, xy
pbc                      = no
periodic_molecules       = no
; nblist cut-off
rlist                    = 0
; long-range cut-off for switched potentials
rlistlong                = -1

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = cut-off
rcoulomb-switch          = 0
rcoulomb                 = 0
; Relative dielectric constant for the medium and the reaction field
epsilon_r                = 1
epsilon_rf               = 1
; Method for doing Van der Waals
; Method for doing Van der Waals
vdw-type                 = Cut-off
; cut-off lengths
rvdw-switch              = 0
rvdw                     = 0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = No


; IMPLICIT SOLVENT ALGORITHM
implicit_solvent         = GBSA

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm             = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii               = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii                 = 0
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent       = 80
; Salt concentration in M for Generalized Born models
gb_saltconc              = 0.150
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha             = 1
gb_obc_beta              = 0.8
gb_obc_gamma             = 4.85
gb_dielectric_offset     = 0.009
sa_algorithm             = Ace-approximation
sa_surface_tension       = -1



Some idea about the implicit solvent setup will be appreciated.
Sanku
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Re: [gmx-users] mdp option for implicit solvent simulation

[Sanku M]

Hi Erik,
  That statement was a typo. The simulation will be done in implicit solvent ( 
not in gas phase).
Sanku



 From: Erik Marklund er...@xray.bmc.uu.se
To: Sanku M msank...@yahoo.com; Discussion list for GROMACS users 
gmx-users@gromacs.org 
Sent: Friday, January 11, 2013 5:04 AM
Subject: Re: [gmx-users] mdp option for  implicit solvent simulation
 
Hi,

If you're simulating in the gas-phase, how come you want implicit solvent?

Erik

On Jan 11, 2013, at 5:07 AM, Sanku M wrote:

 Hi,
   I am trying to do implicit solvent simulation for a protein in gas-phase. I 
have a few questions :
 1) should I use sd integrator?
 
 2) should I also use no periodic condition considering continuum dielectric ?
 
 3) in the JCTC 2010 paper by Lindahl and co-worker, it is mentioned that no 
 cutoffs were used for implicit solvent simulations.
  But, again in implicit solvent setup the rgblist should be equal to rlist.
 Now, if I use rlist=0 ( as all interactions are considered), should I also 
 make rgblist=0?
 Does it mean the setup was following type: i.e.
 
   ; NEIGHBORSEARCHING PARAMETERS
 ; nblist update frequency
 nstlist                  = 0
 ; ns algorithm (simple or grid)
 ns-type                  = simple
 ; Periodic boundary conditions: xyz, no, xy
 pbc                      = no
 periodic_molecules       = no
 ; nblist cut-off
 rlist                    = 0
 ; long-range cut-off for switched potentials
 rlistlong                = -1
 
 ; OPTIONS FOR ELECTROSTATICS AND VDW
 ; Method for doing electrostatics
 coulombtype              = cut-off
 rcoulomb-switch          = 0
 rcoulomb                 = 0
 ; Relative dielectric constant for the medium and the reaction field
 epsilon_r                = 1
 epsilon_rf               = 1
 ; Method for doing Van der Waals
 ; Method for doing Van der Waals
 vdw-type                 = Cut-off
 ; cut-off lengths
 rvdw-switch              = 0
 rvdw                     = 0
 ; Apply long range dispersion corrections for Energy and Pressure
 DispCorr                 = No
 
 
 ; IMPLICIT SOLVENT ALGORITHM
 implicit_solvent         = GBSA
 
 ; GENERALIZED BORN ELECTROSTATICS
 ; Algorithm for calculating Born radii
 gb_algorithm             = Still
 ; Frequency of calculating the Born radii inside rlist
 nstgbradii               = 1
 ; Cutoff for Born radii calculation; the contribution from atoms
 ; between rlist and rgbradii is updated every nstlist steps
 rgbradii                 = 0
 ; Dielectric coefficient of the implicit solvent
 gb_epsilon_solvent       = 80
 ; Salt concentration in M for Generalized Born models
 gb_saltconc              = 0.150
 ; Scaling factors used in the OBC GB model. Default values are OBC(II)
 gb_obc_alpha             = 1
 gb_obc_beta              = 0.8
 gb_obc_gamma             = 4.85
 gb_dielectric_offset     = 0.009
 sa_algorithm             = Ace-approximation
 sa_surface_tension       = -1
 
 
 
 Some idea about the implicit solvent setup will be appreciated.
 Sanku
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[gmx-users] Removing external bias apart from umbrella potential

[Sanku M]

Hi,

I am recently trying to perform an umbrella sampling simulation along a 
particular reaction coordinate on a system where I have also put position 
restraint on certain atoms of the system... So, for each umbrella sampling 
window, I have an extra potential on certain atoms ( due to the position 
restraint ) apart from the umbrella potential. I am using Gromacs4.5.4 for the 
simulation.

So, after carrying out the umbrella sampling simulation, if I use WHAM  to 
remove the bias,  I think  WHAM, in its present implementation,  can only 
remove the bias due to the umbrella potential. But the bias required for 
position-restraining certain atoms remains still there in the computed PMF.

So, I was wondering whether you can suggest any way-out for removing that bias 
from the PMF due to position restraints  as well. 


Sanku

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[gmx-users] PMF and jacobian correction

[Sanku M]

Dear Gromacs user,
  I was having a question on when need to use jacobian coorection of -2KTln(r) 
( gromacs manual chapter 6) term when calculating PMF. I understand for a 
3-dimensional radial coordinate like distance between two groups, this term 
need to taken care of. But, if the PMF is computed along Radius of gyration 
which is an internal coordinate, I was wondering whether this jacobian 
correction still needs to be subtracted.
Any help in sorting out this confusion will be appreciated.
Sanku
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[gmx-users] query on OPLS-2005

[Sanku M]

Hi,
  I wanted to check what is actually OPLS-2005 forcefield that is recently 
being referred often for md simulation. However, I also see that whenever, 
OPLS-2005 is being referred, it cites a 2001 paper by Jorgensen on OPLS 
forcefield. So, what is actually OPLS-2005?
So, I wonder what version of OPLS forcefield is present in gromacs 4.5 series. 
Is it also so-called OPLS-2005 forcefield?
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[gmx-users] How to convert a gromacs trajectory to Desmond trajectory format

[Sanku M]

Hi,
    I was looking for some way out for converting the trajectory-files back and 
forth between two softwares between gromacs and Desmond. 
More specifically, if I run a simulation for a particular system using gromacs 
4.5.4 , how can I convert it into Desmond trajectory file format ?

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Re: [gmx-users] How to convert a gromacs trajectory to Desmond trajectory format

[Sanku M]

Do you mean converting the gromacs trajectory into pdb file and using vmd to 
convert the pdb into desmond trajectory ?




From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thursday, October 27, 2011 7:16 PM
Subject: Re: [gmx-users] How to convert a gromacs trajectory to Desmond 
trajectory format


On 28/10/2011 9:46 AM, Sanku M wrote: 
Hi,
    I was looking for some way out for converting the trajectory-files back 
and forth between two softwares between gromacs and Desmond. 
More specifically, if I run a simulation for a particular system using gromacs 
4.5.4 , how can I convert it into Desmond trajectory file format ?
There are so many interconversion tools that there must be some
intermediate format that both can read and write. At worst, PDB.

Mark 
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[gmx-users] problem with compiling fftw

[Sanku M]

Hi,
  When trying to compile fftw3.3.3 in our cluster I got following error. 
Apparently, it try to guess the build-type by trying to create a directory in 
scratch. I am not sure why it will try to create a directory there and then it 
fails. I was wondering whether there is any way-out to avoid this issue. Is 
there any way in a machine to know its build type and if so, what is the option 
in fftw to mention the directory.
Below is the error message.
Sanku

./configure --prefix=/home/joe/UTIL/fftw/ CC=gcc  --enable-float
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... mkdir: cannot create directory 
`/scratch/cg29917-21909': Permission denied
mkdir: cannot create directory `/scratch/cg-29917': Permission denied
config.guess: cannot create a temporary directory in /scratch
configure: error: cannot guess build type; you must specify one
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Re: [gmx-users] query on OPLS-2005

[Sanku M]

Hi Cara,
   Thanks for a  very clarifying email. It helps a lot.
Sanku



From: Cara Kreck cara_...@hotmail.com
To: gmx-users@gromacs.org
Sent: Friday, October 28, 2011 3:50 AM
Subject: RE: [gmx-users] query on OPLS-2005


 
 
Hi Sanku

According to the Schrodinger Knowledge Base, this is the paper that should be 
referenced for OPLS-2005 instead:
Banks, J.L., H.S. Beard, Y. Cao, A.E. Cho, W. Damm, R. Farid, A.K. Felts,T.A. 
Halgren, D.T. Mainz, J.R. Maple, R. Murphy, D.M. Philipp, M.P. Repasky,L.Y. 
Zhang, B.J. Berne, R.A. Friesner, E. Gallicchio, and R.M. Levy. Integrated 
Modeling Program, Applied Chemical Theory (IMPACT). J. Comp. Chem., 26, 1752 
(2005)
(http://onlinelibrary.wiley.com/doi/10.1002/jcc.20292/full)

The Gromacs oplsaa.ff/forcefield.doc file says OPLS-AA/L all-atom force field 
(2001 aminoacid dihedrals)

OPLS-AA/L seems to presented in the above paper as their updated version, but 
it is sourced from the 2001 paper on proteins which is listed as a reference in 
the Gromacs oplsaa.ff/forcefield.itp file. The 2005 paper then adds  the 
following:
New force-field parameters were developed for OPLS_2003 for organic 
functional groups for which the OPLS_2001 force field does not provide 
specific parameters. Previously derived parameters for proteins, discussed 
above, were implemented without modification in OPLS_2003. (Where 2003 
apparently evolved into 2005).

So it looks like the protein section of both force-fields are the same, but if 
you want to use other parameters you should check them individually first to 
see whether or not they were changed or created since 2001.

Cara






Date: Wed, 26 Oct 2011 15:02:07 -0700
From: msank...@yahoo.com
To: gmx-users@gromacs.org
Subject: [gmx-users] query on OPLS-2005


Hi,
  I wanted to check what is actually OPLS-2005 forcefield that is recently 
being referred often for md simulation. However, I also see that whenever, 
OPLS-2005 is being referred, it cites a 2001 paper by Jorgensen on OPLS 
forcefield. So, what is actually OPLS-2005?
So, I wonder what version of OPLS forcefield is present in gromacs 4.5 series. 
Is it also so-called OPLS-2005 forcefield?
Sanku
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[gmx-users] pdb2gmx problem with ACE N-cap

[Sanku M]

Hi,
  I have a protein pdb file with ACE as N-cap and I am trying to use pdb2gmx ( 
within gromacs 4.5.4 ) to generate a topology file using opls/AA . the ACE is 
present in opls aminoacids.rtp files. But, on issuing the pdb2gmx command, I 
get following error message:

Program pdb2gmx_44, VERSION 4.5.4
Source code file: pdb2top.c, line: 1070

Fatal error:
atom N not found in buiding block 1ACE while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I wonder how I can make sure that ACE can be used as N-terminus.

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[gmx-users] problem with Threading during run

[Sanku M]

Hi,
 I just compiled gromacs 4.5.4 in a cluster. But, I find that if I try to make 
use of threading introduced in gromacs 4.5.x series, it does not work. 
 After issuing command like mdrun -v -s , I expected that for my 8-core 
processor which is not running any other jobs, the threading will show one job 
with 800 % cpu usage. But, it is showing 100 % cpu usage hence using only 1 of 
the 8 processors. I was wondering whether there is any command line I need to 
use to ensure the gromacs understands that there is 8 processors in a core and 
force make full use of the entire machine.

I have tried the same thing in another different cluster where I found that 
threading works with showing 800 % cpu usage . But, for this cluster , the 
threading does not work.

Any help will be appreciated.

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[gmx-users] Jarzinsky's inequality from SMD simulation

[Sanku M]

Hi,
  I have done some steered MD simulation and I want to construct the potential 
of mean force from these pull-profile using Jarzinsky's inequality. I wanted to 
see whether, in updated version of gromacs, there is any implementation of  
extracting PMF from SMD simulations. 
If not, can anyone suggest some guidelines how to do it.
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Re: [gmx-users] Jarzinsky's inequality from SMD simulation

[Sanku M]

Hi Laura,
  I do not think Justin Lemkul's tutorial is suggesting extracting PMF using 
SMD simulation. What is does that it uses SMD to generate the initial 
configurations for different windows and then perform umbrella sampling 
separately on each windows to subsequently extract the PMF using WHAM based on 
the data set on umbrella sampling.

Sanku



From: Laura Kingsley lking...@purdue.edu
To: gmx-users@gromacs.org
Sent: Monday, October 31, 2011 11:09 AM
Subject: Re: [gmx-users] Jarzinsky's inequality from SMD simulation


There is a way to extract the PMF from sMD simulations using the weighted 
histogram analysis method (WHAM) in gromacs- Justin Lemkul's tutorial does a 
nice job of explaining it:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

- Laura



On 10/31/2011 11:05 AM, Sanku M wrote: 
Hi,
  I have done some steered MD simulation and I want to construct the potential 
of mean force from these pull-profile using Jarzinsky's inequality. I wanted 
to see whether, in updated version of gromacs, there is any implementation of  
extracting PMF from SMD simulations. 
If not, can anyone suggest some guidelines how to do it.
Sanku

-- 
Laura Kingsley Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University 
Office: RHPH 504A 
575 Stadium Mall Dr.
West Lafayette, IN 47907
Office Phone: (765) 496-6643
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[gmx-users] Steered MD in reverse direction?

[Sanku M]

Hi,
  I am performing steered Molecular dynamics simulation to pull a molecule out 
of a complex. I am using gromacs 4.5.4 to perform the constant rate pulling..I 
have done the steered MD simulation in a particular direction i.e hav pulled 
the molecule out of complex.
But, to check the convergence/hysterisis of the pulled path way, I would like 
to perform the same steered MD in reverse direction i.e push the molecule back 
into the complex. But, I was wondering, to perform the backward steered MD, how 
should I modify the .mdp parameters?  Should I make the pull_rate1 negative or 
switch the pull_group0 and pull_group1 ?  Any help will be appreciated.

The following is the part of the pull-code parameter I am using:
; Pull code
pull            = umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim        = N N Y
pull_start      = yes       ; define initial COM distance  0
pull_ngroups    = 1
pull_group0     = Mol_A
pull_group1     = Mol_B
pull_rate1      = 0.0025      ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 1000      ; kJ mol^-1 nm^-2
  

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Re: [gmx-users] Steered MD in reverse direction?

[Sanku M]

Thanks for the suggestion.
 Also, I was wondering how one can get the time profile of the irreversible 
work from the gromacs pull-code out put . From constant pulling-rate SMD, we 
get time profile of force pullf.xvg and pullx.xvg. I wonder does multiplying 
the the value from pullx.xvg and value from pullf.xvg will provide the work . 
Or, will it be force ( obtained from pullf.xvg) multiplied by pulling rate 
multiplied by time ?



From: Justin A. Lemkul jalem...@vt.edu
To: Sanku M msank...@yahoo.com; Discussion list for GROMACS users 
gmx-users@gromacs.org
Sent: Thursday, November 3, 2011 9:27 PM
Subject: Re: [gmx-users] Steered MD in reverse direction?



Sanku M wrote:
 Hi,
   I am performing steered Molecular dynamics simulation to pull a molecule 
out of a complex. I am using gromacs 4.5.4 to perform the constant rate 
pulling..I have done the steered MD simulation in a particular direction i.e 
hav pulled the molecule out of complex.
 But, to check the convergence/hysterisis of the pulled path way, I would like 
 to perform the same steered MD in reverse direction i.e push the molecule 
 back into the complex. But, I was wondering, to perform the backward steered 
 MD, how should I modify the .mdp parameters?  Should I make the pull_rate1 
 negative or switch the pull_group0 and pull_group1 ?  Any help will be 
 appreciated.
 

Use a negative pull rate.  But simple pulling like this can be difficult; 
you're now trying to hit a moving target.  A slight rotation of the protein can 
render the whole simulation junk - your pulled molecule may smack into some 
undesired location.

-Justin

 The following is the part of the pull-code parameter I am using:
 ; Pull code
 pull            = umbrella
 pull_geometry   = distance  ; simple distance increase
 pull_dim        = N N Y
 pull_start      = yes       ; define initial COM distance  0
 pull_ngroups    = 1
 pull_group0     = Mol_A
 pull_group1     = Mol_B
 pull_rate1      = 0.0025      ; 0.01 nm per ps = 10 nm per ns
 pull_k1         = 1000      ; kJ mol^-1 nm^-2
  
 Sanku
 

-- 

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] Steered MD in reverse direction?

[Sanku M]

Thanks for the suggestion.
 Also, I was wondering how one can get the time profile of the irreversible 
work from the gromacs pull-code out put . From constant pulling-rate SMD, we 
get time profile of force pullf.xvg and pullx.xvg. I wonder does multiplying 
the the value from pullx.xvg and value from pullf.xvg will provide the work . 
Or, will it be force ( obtained from pullf.xvg) multiplied by pulling rate 
multiplied by time ?



From: Justin A. Lemkul jalem...@vt.edu
To: Sanku M msank...@yahoo.com; Discussion list for GROMACS users 
gmx-users@gromacs.org
Sent: Thursday, November 3, 2011 9:27 PM
Subject: Re: [gmx-users] Steered MD in reverse direction?



Sanku M wrote:
 Hi,
   I am performing steered Molecular dynamics simulation to pull a molecule 
out of a complex. I am using gromacs 4.5.4 to perform the constant rate 
pulling..I have done the steered MD simulation in a particular direction i.e 
hav pulled the molecule out of complex.
 But, to check the convergence/hysterisis of the pulled path way, I would like 
 to perform the same steered MD in reverse direction i.e push the molecule 
 back into the complex. But, I was wondering, to perform the backward steered 
 MD, how should I modify the .mdp parameters?  Should I make the pull_rate1 
 negative or switch the pull_group0 and pull_group1 ?  Any help will be 
 appreciated.
 

Use a negative pull rate.  But simple pulling like this can be difficult; 
you're now trying to hit a moving target.  A slight rotation of the protein can 
render the whole simulation junk - your pulled molecule may smack into some 
undesired location.

-Justin

 The following is the part of the pull-code parameter I am using:
 ; Pull code
 pull            = umbrella
 pull_geometry   = distance  ; simple distance increase
 pull_dim        = N N Y
 pull_start      = yes       ; define initial COM distance  0
 pull_ngroups    = 1
 pull_group0     = Mol_A
 pull_group1     = Mol_B
 pull_rate1      = 0.0025      ; 0.01 nm per ps = 10 nm per ns
 pull_k1         = 1000      ; kJ mol^-1 nm^-2
  
 Sanku
 

-- 

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] How to calculate work

[Sanku M]

Hi,
I am performing steered MD simulation using gromacs.
 I was wondering how one can get the time profile of the irreversible work from 
the gromacs pull-code out put . From constant pulling-rate SMD, we get time 
profile of force pullf.xvg and pullx.xvg. I wonder does multiplying the the 
value from pullx.xvg and value from pullf.xvg will provide the work . Or, will 
it be force ( obtained from pullf.xvg) multiplied by pulling rate multiplied by 
time ?

Sanku-- 
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Re: [gmx-users] Gromacs error message

[Sanku M]

Did you create/have any .mdp file called 'minim.mdp' . The grompp is looking 
for the run parameter file and not finding it as you may not have created one.




From: Salvatore Guccione gucci...@unict.it
To: gmx-users@gromacs.org
Sent: Saturday, November 5, 2011 2:33 PM
Subject: [gmx-users] Gromacs error  message

The below steps were followed to perform the  simulation:
1st) a topology file was generated
(http://www.psc.edu/general/software/packages/gromacs/online/top.html.top)
from the pdb-file (.pdb) by the pdb2gmx program;2nd)  the complex was solvated
using the programs editconf and genbox.
Finally the ions were added by the preprocessing grompp (command: grompp -f
minim.mdp -c solv.gro -p topol.top -o ions.tpr)but  the below error message was 
displaied:
Program grompp, VERSION 4.5.3
Source code file: futil.c, line: 491
File input/output error:
minim.mdp
Thanks in advance for any your help.
Look forward to hearing from you.



Universita' di Catania - A.P.Se.Ma.
Servizio di Posta Elettronica


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[gmx-users] g_wham and entropic subtraction

[Sanku M]

Hi,
  I just wanted to check whether g_wham ( in gromacs4.5.4) already subtract the 
entropic contribution ( -2KTlog(r) term ) term when unbiasing the histogram 
obtained from umbrella sampling using distance in 3D as a reaction coordinate.
Thanks
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[gmx-users] Query on restraining center of mass of a protein

[Sanku M]

Hi,
  I have a system containing water and a large protein. In the simulation, I do 
not want the protein center of mass to drift away. I was wondering what will be 
the reasonable method in gromacs to fix the position of the center of mass of 
the protein in its original position . I was thinking about two options in 
gromacs.
  1) use the protein as comm-grp only to remove its center of mass motion . ( 
or should I use both protein and non-protein ( water) center of mass as 
comm-grps separately ).
  2) Finding the residue closest to center of mass of the protein ( but I am 
not sure how to do it ).
Can anyone suggest which will be a good idea ?

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[gmx-users] query on partial charge entry in topology

[Sanku M]

Hi,
  I find that in the ffnonbonded.itp under OPLS forcefield ( inside opls.ff 
directory), for each particle-type, there is a partial charge assigned to it. 
However, again in the .rtp file, for each residue, under each charge group, 
each of the atom is assigned 
another partial charge assigned to it. I wonder what are the purposes of having 
two partial charge entries and which charge is actually being used in 
simulation . My guess is that , the charge distribution assigned in the .rtp 
file is most probably the one being used during simulation. If so, then what is 
the purpose of having another partial charge entry in the ffnonbonded.itp.
If someone can clarify the doubt, that will be great.

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[gmx-users] density of confined water

[Sanku M]

Hi,
  I would like to know if there is a way in gromacs to calculate the 
time-averaged density of solvent which is confined between two objects , say, 
two plates or another example will be water confined between ligand and 
binding-pocket.
I was thinking about two ways for going about this but in both cases there are 
some issues:
1. I found there is a tool g_densmap but it gives a 2D density map. But, in 
this case, I guess, 3D map would have been necessary.

 2. Also, I found trjorder with -nshell option can calculate number of waters 
within a distance (with -r option) . But, in this case, I need to know volume 
of the confined space as well. I am not sure gromacs can calculate the volume 
of the confined space.

Any help or suggestion of  any other suitable  methods will be highly 
appreciated.

Sanku
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[gmx-users] output logfile

[Sanku M]

Hi,
 It might be a very minor issue but I find in versions of gromacs 4.5.4, the 
output log file ( in verbose mode) writes the progress of the simulation in a 
single line ( unlike in previous gromacs 4.0.7 version) where it used to write 
the progress in a new lines. As a result, in gromacs4.5.4, opening a logfile or 
issuing unix 'tail' command to see last few lines becomes a bit time-consuming 
as the progress is written in a single line.

An example is shown below for gromacs 4.5.4:
  ^Mstep 2100, will finish Sat Dec  3 19:55:12 2011vol 0.79  imb F  0% ^Mstep 
2200, will finish Sat Dec  3 19:54:59 2011vol 0.80  imb F  1% ^Mstep 2300, will 
finish Sat Dec  3 19:54:49 2011vol 0.79  imb F  1% ^Mstep 2400, will finish Sat 
Dec  3 19:54:40 2011vol 0.80  imb F  0% ^Mstep 2500, will finish Sat Dec  3 
19:54:31 2011vol 0.80  imb F  1% ^Mstep 2600, will finish Sat Dec  3 19:54:22 
2011vol 0.80  imb F  1% ^Mstep 2700, will finish Sat Dec  3

I wonder whether there is an fix for this minor issue. 

Thanks
Sanku
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Re: [gmx-users] output logfile

[Sanku M]

Hi,
  This has been compiled and installed in same machine which runs Linux. It 
never happens in any other version lower than gromacs4.5.
Sanku



 From: Broadbent, Richard richard.broadben...@imperial.ac.uk
To: Sanku M msank...@yahoo.com; Discussion list for GROMACS users 
gmx-users@gromacs.org 
Sent: Saturday, December 3, 2011 7:24 PM
Subject: Re: [gmx-users] output logfile 
 

Re: [gmx-users] output logfile 
Hi Sanku

The ^M ‘s in that sample indicate a line break that was issued by a different 
text formatting standard. This frequently happens if files are generated in one 
OS say Windows then viewed in another say unix. Is your version of gromacs 
compiled for your system
 or was is compiled for a different machine/OS?

Richard


On 03/12/2011 19:50, Sanku M msank...@yahoo.com wrote:

 
Hi,
 It might be a very minor issue but I find in versions of gromacs 4.5.4, the 
output log file ( in verbose mode) writes the progress of the simulation in a 
single line ( unlike in previous gromacs 4.0.7 version) where it used to write 
the progress in a new lines.
 As a result, in gromacs4.5.4, opening a logfile or issuing unix 'tail' command 
to see last few lines becomes a bit time-consuming as the progress is written 
in a single line.

An example is shown below for gromacs 4.5.4:
  ^Mstep 2100, will finish Sat Dec  3 19:55:12 2011vol 0.79  imb F  0% ^Mstep 
2200, will finish Sat Dec  3 19:54:59 2011vol 0.80  imb F  1% ^Mstep 2300, 
will finish Sat Dec  3 19:54:49 2011vol 0.79  imb F  1% ^Mstep 2400, will 
finish Sat Dec  3 19:54:40 2011vol
 0.80  imb F  0% ^Mstep 2500, will finish Sat Dec  3 19:54:31 2011vol 0.80  imb 
F  1% ^Mstep 2600, will finish Sat Dec  3 19:54:22 2011vol 0.80  imb F  1% 
^Mstep 2700, will finish Sat Dec  3

I wonder whether there is an fix for this minor issue. 

Thanks
Sanku



 
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[gmx-users] good reference for PCA in gromacs

[Sanku M]

Hi,
  I am wondering whether someone can suggest a reference paper based on which 
all gromacs principal component analysis (PCA) analysis ( i.e g_covar and 
g_anaeig tools) tools are based . Or, any other review articles on  PCA 
analysis  is based will also be useful.
Thanks
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[gmx-users] umbrella sampling with replica exchange

[Sanku M]

Hi,
  I have a technical question regarding feasibility of  combining replica 
exchange with umbrella sampling or any other pulling simulations in gromacs.
Since the umbrella sampling or any other pulling simulations are 
non-equilibrium simulation due to presence of external bias, I wonder whether 
the detailed balance in  replica exchange simulation  will be maintained .
I ask this because replica exchange  uses Monte Carlo metropolis algorithm to 
swap configurations and so I wanted to know what is the energy-difference ( New 
energy - old energy) in metropolis algorithm gromacs will use : Is it the 
energy difference after taking into account the biasing potential or is is only 
the internal potential energy-difference ( i.e not including biasing potential 
) ?

Any response from the users or developer will be highly appreciated.

Thanks

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[gmx-users] combining umbrella sampling with replica exchange

[Sanku M]

Hi,
  I sent this email few weeks back and thought sending it again in case someone 
can give some opinion.
I have a technical question regarding feasibility of  combining replica 
exchange with umbrella sampling or any other pulling simulations in gromacs.
Since the umbrella sampling or any other pulling simulations are 
non-equilibrium simulation due to presence of external bias, I wonder whether 
the detailed balance in  replica exchange simulation  will be maintained .
I ask this because replica exchange  uses Monte Carlo metropolis algorithm to 
swap configurations and so I wanted to know what is the energy-difference ( New 
energy - old energy) in metropolis algorithm gromacs will use : Is it the 
energy difference after taking into account the biasing potential or is is only 
the internal potential energy-difference ( i.e not including biasing potential 
) ?

Any response from the users or developer will be highly appreciated.

Thanks
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[gmx-users] average force on solute

[Sanku M]

Hi,
  I am simulating a peptide in a box of water in gromacs 4.5.4 . From the 
trajectory, I want to compute the time-averaged force acting on the peptide. 
I found g_traj tool can provide information on force upon supplying the 
traj.trr file  and g_traj help menu also suggests that using -af option one can 
get the average force on a selected group.
But, I found a problem in executing the g_traj tool to calculate the average 
force. I find that  if the .trr file do not store any coordinate ( but store 
only force), then the -af option actually do not work.

Since  I was interested in force, in my mdp output file option,I used following 
settings i.e in the .trr file I only write the force.

 Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 0
nstvout                  = 0
nstfout                  = 5
; Output frequency for energies to log file and energy file
nstlog                   = 5
nstcalcenergy            = -1
nstenergy                = 5000
; Output frequency and precision for .xtc file
nstxtcout                = 1000
xtc_precision            = 1000

But, after running the simulation,  if I try to use g_traj to extract the 
force,using following command:
 g_traj_44 -f traj.trr -s -n  -af  -cf

I get following warning and no average force is being written:

WARNING: No coordinate frames found for option -cv or -cf

No frames found for average force, will not write force.pdb

I wonder, why one need to have coordinate stored as well to get the average 
force file or there is any other work-around for this or do I really need to 
also store coordinates in the trr file for getting the average force.


If there is any other alternatives for getting the average force, please let me 
know.

Thanks
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[gmx-users] How to find Hbonding partner

[Sanku M]

Hi,
   I am wondering whether there is any way in GROMACS that one can find which 
groups are the main Hbonding partners in a trajectory. For example, if I 
simulate a peptide in water, I want to know during the simulation, which 
particular atoms in the peptides are making most of the Hbonds with water as a 
function of time. I find g_hbond can tell us the total number of Hbond between 
two groups as a function of time but, can it specify which groups are making 
the Hbonds most of the time ?

Any help will be appreciated.

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[gmx-users] query on g_sorient

[Sanku M]

Hi,

  I am trying to understand what are the angles g_sorient plans to compute. 
The manual says that the theta1 is the angle with the vector from the first 
atom of the solvent molecule
to the midpoint between atoms 2 and 3 .  But, I wonder what is the reference 
position of this angle  ? In other words, what is the 3rd atom that one needs 
for the calculation angle ( the first atom being the water-oxygen, second atom 
being the  
midpoint of two water-hydrogen) ?  Is the 3rd atom any solute atom or their 
center of mass ?


Thanks
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[gmx-users] FEP for ligand mutation

[Sanku M]

Hi,
  Is it possible in GROMACS4.5 to perform computation of relative binding free 
energy of a ligand to a protein due to mutation in the ligand ( or due tio 
mutation in the protein)? 
I have done the computation of solvation free energy of a solute in a solvent 
using FEP but looking for some suggestions or tutorial on how to compute the 
relative binding free energy in a protein-ligand system.
Any help will be appreciated.
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[gmx-users] gromacs installation with mpi

[Sanku M]

Hi,
 I am using a cluster where user/local/bin has some old mpi executable. But, I 
have installed openmpi-1.3 in my own home directory so that I can use that for 
installing gromacs4.5.4 parallel version. I have also updated the path with the 
openmpi bin directory and library directory in the bash profile.

But, each time, I try to configure gromacs4.5.4 using enable-mpi mode, it 
always looks into the mpi installed in /usr/local/bin directory anad crashes 
saying that the mpicc is not compatible.
I wonder whether there is any particular flag I can use so that I can force 
gromacs to look for openmpi bin and lib folder installed in my home directory.
Thanks
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[gmx-users] cutting a cylinder from simulation box

[Sanku M]

Hi,
  I have run a simulation of a fixed object in water using gromacs. Now, I want 
to analyze only water molecules which are present within a cylinder of certain 
radius (smaller than simulation box dimension in XY plane).
I wonder whether gromacs has any particular tool which can identify the 
particles within a cylindrical volume of a simulation box.
Thanks
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[gmx-users] Umbrella sampling along Radius of gyration

[Sanku M]

Hi,
  Is there any way in gromacs to use radius of gyration of a polymer as 
reaction coordinate for umbrella sampling ?
Thanks
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[gmx-users] Charmm27.ff with FEP

[Sanku M]

Hi,
 Is there any known issue/problem in running FEP calculations with charm27.ff 
in gromacs4.5.4 ? I tried running an FEP calculation using charmm27.ff by 
interpolating A state and B state but it gives error that dihedral terms with 
multiple values can not be interpolated..One need to write all A and B states 
in topol.top manully.
With opls.ff , it does not have any such problem.
Any idea?
Thanks
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[gmx-users] problem with NVE ensemble simulation with Martini lipid

[Sanku M]

Hi,
  I am having a problem with running a NVE ( micro-canonical) ensemble  using a 
system of 128 Martini DPPC lipids. I started the simulation with a 128 lipid 
bilayer with Martini water  which was pre-equilibrated in NPT ensemble ( using 
berendsen  temperature coupling at 325 K( separate coupling for lipid and 
water) and  pressure coupling at 1 atm for 500 ns).
But, when I started running the NVE simulation by switching off pressure 
coupling and temperature coupling, the temperature started going down from 325 
to almost 2 K very quickly which looks like very unphysical. However, total 
energy remains conserved . But the temperature is becoming a concern as it is 
going down to a 0 K.   I am not sure whether I am doing some mistake in the mdp 
parameter. Any help will be appreciated.

Here is the part of  mdp option I used for running with gromacs-4.0.7

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0.0
dt   = 0.020
nsteps   = 2500
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files separate)
simulation_part  = 1
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= DPPC Nonlipid

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric  = 0
ld-seed  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 10
emstep   = 0.01
; Max number of iterations in relax_shells
niter= 20
; Step size (ps^2) for minimization of flexible constraints
fcstep   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep   = 1000
nbfgscorr= 10

; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 500
nstvout  = 500
nstfout  = 0
; Output frequency for energies to log file and energy file
nstlog   = 500
nstenergy= 500
; Output frequency and precision for xtc file
nstxtcout= 500
xtc_precision= 100
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps   = DPPC Nonlipid

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 10
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1.4

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 15
epsilon_rf   = 1
; Method for doing Van der Waals
vdw_type = Shift
; cut-off lengths
rvdw_switch  = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; 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
; Temperature coupling
tcoupl   = no
; Groups to couple separately
tc-grps  =
; Time constant (ps) and reference temperature (K)
tau-t=
ref-t=
; Pressure coupling
Pcoupl   = no

; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p= 1
compressibility  =
ref-p=
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = No
; Random seed for Andersen thermostat
andersen_seed= 815131
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel  = yes
gen_temp = 325
gen_seed = 473529

; OPTIONS FOR BONDS
constraints  = none
; Type of constraint algorithm
constraint_algorithm = Lincs
; Do not constrain the start 

[gmx-users] how to calculate diffusion constant of the entire lipid-bilayer

[Sanku M]

Hi,
  I was interested in calculating the diffusion constant of the center of mass 
of entire lipid-bilayer ( not individual lipid molecules).   Regarding this, I 
had two doubts I wanted to clarify:
   1. Since I am interested in calculating the diffusion constant of the 
bilayer iteself, I guess I should  allow the drift of the bilayer and hence  
not then remove the center of mass motion of bilayer (and solvent ) separately. 
Is that right ?  If so, is it still OK to remove the center of mass of whole 
system ( bilayer + water together ) ? 

2.   How to calculate the mean square displacement of  center of mass  of the 
entire bilayer. I guess, g_msd program  by default, calculate  the diffusion 
constant of the individual atoms or molecules.But, is there a way to get 
the diffusion constant of the entire bilayer center of mass ?  If I specify the 
index group which consist of all the atoms of the bilayer, will g_msd provide 
the diffusion constant of its center of mass or it will give the diffusion 
constant of individual atoms ?  I guess, in that case, one should not use 
-rmcomm option . Is that right ?



Thanks
Jagannath


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[gmx-users] query on constraint-force pull code

[Sanku M]

Hi,
  I would like to use constraint force pull code to calculate the free energy 
of association of two peptide  using the distance between center of mass of two 
peptides as reaction coordinate. I am planning to use gromacs 4. 
Here I have some queries:
1. Since I will constraint method, I guess,  I do not have to use any 
force-constant ( unlike umbrella sampling) . If that is correct, do I need to 
specify a pulling rate ? If so, what will be a typically appropriate range of 
value to start with ?

2. In umbrella sampling technique, we check the overlap of position histogram 
of two consecutive windows to check the convergence . Here , using constraint 
force technique, what should I check for convergence. Is that the force ?

3. Once I get time series of force for all windows, how  should I unbias the 
effect of constraint and what formula I should use to integrate the force? Is 
that integration implemented in gromacs ?

Thanks
Sanku



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[gmx-users] free energy : query on constraint force pull code

[Sanku M]

Hi,
  I would like to use constraint force pull code to calculate the free energy 
of association of two peptide  using the distance between center of mass of two 
peptides as reaction coordinate. I am planning to use gromacs 4. 
Here I have some queries:
1. Since I will constraint method, I guess,  I do not have to use any 
force-constant ( unlike umbrella sampling) . If that is correct, do I need to 
specify a pulling rate ? If so, what will be a typically appropriate range of 
value to start with ?

2. In umbrella sampling technique, we check the overlap of position histogram 
of two consecutive windows to check the convergence . Here , using constraint 
force technique, what should I check for convergence. Is that the force ?

3. Once I get time series of force for all windows, how  should I unbias the 
effect of constraint and what formula I should use to integrate the force? Is 
that integration implemented in gromacs ?

Thanks
Sanku


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[gmx-users] large oscillation in mean force with constraint

[Sanku M]

Hi,
  I am trying to calculate the PMF of two peptides using constraint in gromacs 
4.0.5. But, I am finding a very large oscillation( from -1000 to +1000) in the 
force that is being printed in pullf.xvg file . Is this oscillation normal ? In 
that case at any distance, the mean force will be zero ( I assume).

Here is the excerpt of the mdp file:
; pull code
pull = constraint
pull_geometry= distance
pull_dim = Y Y Y
pull_init1   = 1.5
pull_k1  =
pull_group0  = CA1
pull_ngroups = 1
pull_group1  = CA2
pull_nstxout = 50  ;step
pull_nstfout = 20

Thanks
Jagannath


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[gmx-users] How to add an user-defined external potential

[Sanku M]

Hi,
  I am planning to add an external harmonic potential along z direction of a 
system : i.e U(z)= 0.5*K*z(**2)
I was wondering if I can get an help on how to add an user-defined external 
potential like this in gromacs ? 
Thanks
Sanku


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[gmx-users] how to define charge group?

[Sanku M]

Hi,
  I am trying to write a topology in gromacs format for a recently developed 
molecule in OPLS format. From the parameterization-paper, I know the partial 
charges on each of the atom in that molecule from the corresponding paper . 
But, 
I am not sure how to split the molecule topology into several charge-groups. I 
mean, is there any thumb-rule on how to define opls charge groups for using in 
gromacs. Only thing I know from mailing list is that one should not use large 
charge-groups. But, I was wondering if someone can provide some input on how to 
define charge-groups.
Sanku-- 
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[gmx-users] rigid tetrahedral molecule

[Sanku M]

Hi,
 I am interested in simulating a anionic molecule BF4(-)  ( Boron 
tetrafluoride).  In the paper which developed the parameters for this molecule, 
it is mentioned that it has been used as 'rigid' molecule i.e the molecule only 
has non-bonding interaction but there was no intramolecular motion as the 
geometry was fixed.
 I am trying to simulate this molecule in gromacs treating it as rigid.  But, I 
was looking for best way to 'rigidify' this molecule.

I was wondering whether using LINCS to constrain all B-F and F-F bonds will be 
good enough .  Or, Should I use virtual sites ? If I really need to use virtual 
site, will it be something like TIP5P water model ?
  
Can someone suggest the best wayout ?

Sanku-- 
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Re: [gmx-users] rigid tetrahedral molecule

[Sanku M]

Thanks. The molecule was developed as a part of OPLS. The authors used a 
software called BOSS( developed in Bill Jorgensen's lab) . I guess this 
softwares have way to perform rigid body motion. There are other softwares like 
DL-POLY which can perform rigid body MD. So, I guess, in those cases, just 
declaring a molecule 'rigid' might be good enough. 
But, gromacs does not explicitly do rigid body MD. That's why I was looking for 
a trick .





From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wed, April 27, 2011 8:25:05 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule



Sanku M wrote:
 Hi,
  I am interested in simulating a anionic molecule BF4(-)  ( Boron 
tetrafluoride).  In the paper which developed the parameters for this 
molecule, 
it is mentioned that it has been used as 'rigid' molecule i.e the molecule 
only 
has non-bonding interaction but there was no intramolecular motion as the 
geometry was fixed.
  I am trying to simulate this molecule in gromacs treating it as rigid.  But, 
 I 
was looking for best way to 'rigidify' this molecule.
 
 I was wondering whether using LINCS to constrain all B-F and F-F bonds will 
 be 
good enough .  Or, Should I use virtual sites ? If I really need to use 
virtual 
site, will it be something like TIP5P water model ?
   Can someone suggest the best wayout ?
 

Constraints should do the trick, but probably the best approach is to simply 
contact the authors who developed the model and ask how they did it.  Then you 
know you're exactly reproducing what they did.

-Justin

 Sanku


-- 

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] rigid tetrahedral molecule

[Sanku M]

 I went through the LINCS manual .  But, I am still struggling with coming up 
with the idea of putting correct constraint to maintain the rigidity of 
tetrahedral molecule .  I seem to understand  from your suggestion that the 
tetrahedral can be seen as a combination of  4  coupled triangles.( or am I 
still wrong about it ?)
In that case, am I supposed to use multiple settle to keep the molecule in a 
tetrahedral fashion ? I am sorry but if you can explain it in bit more details, 
I might get the point.




From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wed, April 27, 2011 11:14:34 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule

On 4/28/2011 1:54 PM, Sanku M wrote: 
Hi,
  I tried to keep the geometry of the BF4 fixed by using   constraints 
using lincs. But , unfortunately, my simulation is   crashing 
immediately and if I try minimization with only 2   molecules, it 
provides a lot of LINCS warning and generate a   lot of step*.pdb file 
. 
If I try to visualize the minimized   snapshot in VMD, it looks like 
all 
the distances I tried to   constrain decreased drastically. Finally, 
trying MD run with   this minimized configuration results in 
crashing 
due to bad   contacts.


 I am sure I am doing something wrong and it might be that   my itp 
 file 
is wrong . So any help will be highly appreciated.
Here is the details of what I did.


  The geometry of the molecule is tetrahedral with B at   the 
 center 
and 4 F atoms is surrounding it in a tetrahedral   manner.
I first generated a itp file for BF4 which is shown below:   I first 
got 
the LJ parameters and charges for B and F atom and   put them in 
ffoplsnb.itp file as new atom types opls_1014   and opls_1015 
. Initially I tried to put contsraint along all   bonds ( i.e among F 
atoms as well ). But, grompp provides   warning that number of 
constraint is more than number of   degrees of freedom. So, I reduced 
number of constraints by   only putting constraint among B and F. But, 
it did not work   either. 


Sure, you need as many constraints as 
http://en.wikipedia.org/wiki/Degrees_of_freedom_%28physics_and_chemistry%29

You should also do your homework about using LINCS and coupled triangles of 
constraints, as I suggested last time.

Mark


Here is  the .itp file I wrote for rigid BF4 . It will be   great if 
someone can point me what I am doing wrong.


  [ moleculetype ]
; molname   nrexcl
BF4 3


[ atoms ]
#ifdef _FF_OPLS
 1  opls_1014   1BF4B   1  0.8276
 2  opls_1015   1BF4F1  1  -0.4569
 3  opls_1015   1BF4F2  1  -0.4569
 4  opls_1015   1BF4F3  1  -0.4569
 5  opls_1015   1BF4F4  1  -0.4569
#endif
[ constraints ]
  1  2   1   0.146
  1  3   1   0.146
  1  4   1   0.146
  1  5   1   0.146
  ;  2  3   1   0.238
;  2  4   1   0.238
;  2  5   1   0.238
;  3  4   1   0.238
;  3  5   1   0.238
;  4  5   1   0.238


[ exclusions ]
1   2   34  5
2   1   34  5
3   1   24  5
4   1   23  5
5   1   23  4






From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wed,   April 27, 2011 8:39:23 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule

On 4/28/2011 11:25 AM, Justin A. Lemkul wrote:
 
 
 Sanku M wrote:
 Hi,
  I am interested in simulating a anionic molecule BF4(-)  ( 
 Boron 
tetrafluoride).  In the paper which developed the parameters for 
this molecule, it is mentioned that it has been used as 'rigid' 
molecule i.e the molecule only has non-bonding interaction but 
there 
was no intramolecular motion as the geometry was fixed.
  I am trying to simulate this molecule in gromacs treating it 
 as 
rigid.  But, I was looking for best way to 'rigidify' this 
molecule.
 
 I was wondering whether using LINCS to constrain all B-F and 
 F-F 
bonds will be good enough .  Or, Should I use virtual sites ? If 
I 
really need to use virtual site, will it be something like TIP5P 
water model ?
  Can someone suggest the best wayout ?
 
 
 Constraints should do the trick, but probably the best approach 
 is 
to simply contact the authors who developed the model and ask how 
they did it.  Then you know you're exactly reproducing what they 
did.

Yep.

Be aware that the coupled constraints make life tricky, and you 
should read up in the manual and literature for how best to use 
P-LINCS in such cases. Algorithms like SETTLE

Re: [gmx-users] rigid tetrahedral molecule

[Sanku M]

Thanks Mark for your comment. But, as far as degrees of freedom is concerned, 
if 
there is a tetrahedral molecule as I shown below with atom #1 ( B) being center 
of the tetrahedron , if we had defined the molecules in terms of bonds and 
angles ( in stead of constraints ), we would have 4 bonds ( 1-2,1-3,1-4,1-5 ) 
and 6 angles ( 2-1-3,2-1-4,2-1-5,3-1-4,3-1-5 , 4-1-5 )at 109.45 degrees  , thus 
total ( 4+6)=10 descriptors .
In that case, the simulation goes fine . But, then wonder, why, for 
constraints, 
we can put only 9 descriptors .  
Also, I have tried all possible combination to get 9 constraints, but , in each 
case, gromacs crashes. However, defining 4 bonds and 6 angles using high 
force-constant lets the simulation go fine.  So, on a second thought, I wonder 
whether defining 9 bond-constraints to get a stable tetrahedral molecule is at 
all possible. Do I need to go for some sort of compromise,  where 4 bonds 
( 1-2,1-3,1-4,1-5 )  are defined as constraints and 6 angles with high 
force-constant are defined to maintain tetrahedral nature ? 
I am not sure what should be the best possible 9 constraints . 
  1  opls_1014   1BF4B   1  0.8276
 2  opls_1015   1BF4F1  1  -0.4569
 3  opls_1015   1BF4F2  1  -0.4569
 4  opls_1015   1BF4F3  1  -0.4569
 5  opls_1015   1BF4F4  1  -0.4569




From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thu, April 28, 2011 1:00:42 AM
Subject: Re: [gmx-users] rigid tetrahedral molecule

On 4/28/2011 3:49 PM, Sanku M wrote: 
 I went through the LINCS manual .  But, I am still   struggling with 
coming up with the idea of putting correct   constraint to maintain the 
rigidity of tetrahedral molecule .I seem to understand  from your 
suggestion that the   tetrahedral can be seen as a combination of  4 
 coupled   triangles.( or am I still wrong about it ?)
I think it's seven coupled triangles, but that's not a relevant way to 
think 
about it. You have 5 atoms, so 3N-6 means 9 degrees of freedom, so you need 
9 independent descriptors of relative atomic positions, so 9 constraints. 
You were trying 10 and 5.

Because those constraints form triangles, you may need to take care with 
LINCS to get a stable simulation. Read up on the details here, I don't 
remember them.


In that case, am I supposed to use multiple settle to keep   the 
molecule in a tetrahedral fashion ? I am sorry but if you   can explain 
it in bit more details, I might get the point.
Forget about SETTLE - it was just an example to illustrate that this is not 
easy to do right. There's a specialised algorithm for rigid water (with 
three coupled bond constraints) because it is fiddly to get such things 
right (and fast).

Mark




From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wed,   April 27, 2011 11:14:34 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule

On 4/28/2011 1:54 PM, Sanku M wrote: 
Hi,
  I tried to keep the geometry of the BF4 fixed by   using 
constraints using lincs. But , unfortunately, my   simulation 
is 
crashing immediately and if I try   minimization with only 2 
molecules, it provides a lot   of LINCS warning and generate 
a 
lot of step*.pdb file   . If I try to visualize the minimized 
snapshot in VMD,   it looks like all the distances I tried to 
constrain   decreased drastically. Finally, trying MD run 
with   
this minimized configuration results in crashing due   to 
bad 
contacts.


 I am sure I am doing something wrong and it might   be that 
 my 
itp file is wrong . So any help will be   highly appreciated.
Here is the details of what I did.


  The geometry of the molecule is tetrahedral   with B at 
the center and 4 F atoms is surrounding it   in a tetrahedral 
manner.
I first generated a itp file for BF4 which is shown   below: 
I 
first got the LJ parameters and charges for B   and F atom 
and 
put them in ffoplsnb.itp file as new   atom types opls_1014 
and opls_1015 . Initially I tried   to put contsraint along 
all 
bonds ( i.e among F atoms   as well ). But, grompp provides 
warning that number of   constraint is more than number of 
degrees of freedom.   So, I reduced number of constraints by 
only putting   constraint among B and F. But, it did not work 
either. 


Sure, you need as many constraints as 
http://en.wikipedia.org

[gmx-users] vdw cutoff options for opls forcefield

[Sanku M]

Hi,
  I was wondering whether someone can comment on what  vdw-cutoff scheme will 
be 
suitable when using a molecule under OPLS/AA force field . Also, providing some 
details about what cut-off value one should use will be really helpful.
Thanks
Sanku-- 
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Re: [gmx-users] rigid tetrahedral molecule

[Sanku M]

Hi David,
  Actually, I had tried to use vsites to make this molecule rigid. I read the 
manual section 4.7 as well. But, unfortunately, for a 5-site tetrahedral 
geometry I was not able to figure out the right vsite type I should use. So, I 
was wondering whether you can provide some input on the details of how to use 
virtual sites for a tetrahedral molecule.  It would have been helpful.
Sanku




From: David van der Spoel sp...@xray.bmc.uu.se
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Fri, April 29, 2011 11:46:01 AM
Subject: Re: [gmx-users] rigid tetrahedral molecule

On 2011-04-29 17.55, gyorgy.han...@fc.up.pt wrote:

 Hi Sanku,

 I've read about your problem just now, I don't know if it's already
 solved but I had the same problem some weeks ago and I also had a lot of
 troubles. But, finally I managed to solve it so maybe my experiences can
 be helpful for you:

 I think you should use SHAKE instead of LINCS. The manual says somewhere
 that LINCS cannot be used when constraining triangles (i.e. angles) but
 SHAKE works fine. On the other hand, if you use SHAKE you must switch
 from domain decomposition to particle decomposition (if you run your
 simulations parallel) just by using -pd when you type mdrun ('domain
 decomposition = no' in the mdp file is not enough).

 Then you must add as many constraints as degrees of freedom you have, so
 9 in your case. In my case it was 15 for the PF6 anion. Maybe it'll work
 with less than 9 but in my case I had to add 15 contraints. What I did
 was the following:
 First I constrained all P-F bonds then I constrained fictious F-F bonds
 that I thought would make the molecule rigid. But it wasn't enough. Then
 I added some more redundant F-F contraints (up to 15 in total) in a bit
 arbitrary way until I found the 'magic combination'.
 Now my simulations run perfectly.

Please note that if your rigid molecule has less than 6 degrees of 
freedom your temperature will be incorrect!
You can achieve a solution with the right number of d.o.f. by using 
vsites as well. How to do this is left as an exercise for the reader.

 I hope this helps.

 best,
 Gyorgy


 Citando Sanku M msank...@yahoo.com:

 Thanks. The molecule was developed as a part of OPLS. The authors used a
 software called BOSS( developed in Bill Jorgensen's lab) . I guess this
 softwares have way to perform rigid body motion. There are other
 softwares like
 DL-POLY which can perform rigid body MD. So, I guess, in those cases,
 just
 declaring a molecule 'rigid' might be good enough.
 But, gromacs does not explicitly do rigid body MD. That's why I was
 looking for
 a trick .




 
 From: Justin A. Lemkul jalem...@vt.edu
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Sent: Wed, April 27, 2011 8:25:05 PM
 Subject: Re: [gmx-users] rigid tetrahedral molecule



 Sanku M wrote:
 Hi,
 I am interested in simulating a anionic molecule BF4(-) ( Boron
 tetrafluoride). In the paper which developed the parameters for this
 molecule,
 it is mentioned that it has been used as 'rigid' molecule i.e the
 molecule only
 has non-bonding interaction but there was no intramolecular motion as
 the
 geometry was fixed.
 I am trying to simulate this molecule in gromacs treating it as
 rigid. But, I
 was looking for best way to 'rigidify' this molecule.

 I was wondering whether using LINCS to constrain all B-F and F-F
 bonds will be
 good enough . Or, Should I use virtual sites ? If I really need to
 use virtual
 site, will it be something like TIP5P water model ?
 Can someone suggest the best wayout ?


 Constraints should do the trick, but probably the best approach is to
 simply
 contact the authors who developed the model and ask how they did it.
 Then you
 know you're exactly reproducing what they did.

 -Justin

 Sanku


 -- 

 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 list gmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search
 before posting!
 Please don't post (un)subscribe requests to the list. Use the www
 interface or
 send it to gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/Support/Mailing_Lists






-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
-- 
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Please search the archive at 
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before

[gmx-users] trjconv problem

[Sanku M]

Hi,
  I am having a problem with trjconv to get a single snap-shot from a 
trajectory 
file. I am using gromacs 4.0.7 .
If I try to get a snapshot corresponding to 14 ps, I was trying to use  -b 14 
-e 14  command as follows. But,
If I issue this command as shown below
trjconv --f  traj.xtc -o  conf_pep.gro -s topol.tpr  -b 14.0 -e 14.0 
 it crashes with following error:
Precision of traj.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)

WARNING no output, trajectory ended at 14

However, if I issue the same trjconv command using -dump 14 as shown below, 
trjconv provides the correct snapshot at 14 ps:
trjconv --f  traj.xtc -o  conf_pep.gro -s topol.tpr  -dump 14.0 
But, this -dump 14 command becomes extremely time consuming as I was trying 
to 
get the snap-shot for a long time i.e around 3ps . So, I am trying to get 
-b 14 -e 14 command work .So, I was wondering whether you have any clue 
how to get around with this.
Sanku-- 
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Re: [gmx-users] trjconv problem

[Sanku M]

Hi Justin,
  In many of the frames, if I use -b and -e to be same , it works
For example, I found if I use -b 16 -e 16, it gives me the the snapshot at 
16ps. 
 But, in many cases like 14ps, it is not working. Also, I tried -b 13 -e 14 
-dump 14  . It does not work saying 'WARNING no output, trajectory ended at 14'
Any help will be appreciated.
Sanku




From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thu, May 5, 2011 10:22:38 AM
Subject: Re: [gmx-users] trjconv problem



Sanku M wrote:
 Hi,
   I am having a problem with trjconv to get a single snap-shot from a 
trajectory file. I am using gromacs 4.0.7 .
 If I try to get a snapshot corresponding to 14 ps, I was trying to use  -b 
 14 
-e 14  command as follows. But,
 If I issue this command as shown below
 trjconv --f  traj.xtc -o  conf_pep.gro -s topol.tpr  -b 14.0 -e 14.0  it 
crashes with following error:
 Precision of traj.xtc is 0.001 (nm)
 Using output precision of 0.001 (nm)
 
 WARNING no output, trajectory ended at 14
 
 However, if I issue the same trjconv command using -dump 14 as shown below, 
trjconv provides the correct snapshot at 14 ps:
 trjconv --f  traj.xtc -o  conf_pep.gro -s topol.tpr  -dump 14.0 But, this 
-dump 14 command becomes extremely time consuming as I was trying to get the 
snap-shot for a long time i.e around 3ps . So, I am trying to get -b 14 
-e 
14 command work .So, I was wondering whether you have any clue how to get 
around with this.

If I recall, -b and -e cannot be the same.  This is the reason for -dump.  It 
might be worth a try to see if trjconv -b 13 -e 14 -dump 14 speeds things up 
any.

-Justin

 Sanku
 
 

-- 

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] trjconv problem

[Sanku M]

I found it will work if I use -b 13.9 -e 14.1





From: Sanku M msank...@yahoo.com
To: jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thu, May 5, 2011 10:33:19 AM
Subject: Re: [gmx-users] trjconv problem


Hi Justin,
  In many of the frames, if I use -b and -e to be same , it works
For example, I found if I use -b 16 -e 16, it gives me the the snapshot at 
16ps. 
 But, in many cases like 14ps, it is not working. Also, I tried -b 13 -e 14 
-dump 14  . It does not work saying 'WARNING no output, trajectory ended at 14'
Any help will be appreciated.
Sanku




From: Justin A. Lemkul  jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thu, May 5, 2011 10:22:38 AM
Subject: Re: [gmx-users] trjconv problem



Sanku M wrote:
 Hi,
   I am having a problem with trjconv to get a single snap-shot from a 
trajectory file. I am using gromacs 4.0.7 .
 If I try to get a snapshot corresponding to 14 ps, I was trying to use  -b 
 14 
-e 14  command as follows. But,
 If I issue this command as shown below
 trjconv --f  traj.xtc -o  conf_pep.gro -s topol.tpr  -b 14.0 -e 14.0  it 
crashes with following error:
 Precision of traj.xtc is 0.001 (nm)
 Using output precision of 0.001 (nm)
 
 WARNING no output, trajectory ended at 14
 
 However, if I issue the same trjconv command using -dump 14 as shown below, 
trjconv provides the correct snapshot at 14 ps:
 trjconv --f  traj.xtc -o  conf_pep.gro -s topol.tpr  -dump 14.0 But, this 
-dump 14 command becomes extremely time consuming as I was trying to get the 
snap-shot for a long time i.e around  3ps . So, I am trying to get -b 14 
-e 
14 command work .So, I was wondering whether you have any clue how to get 
around with this.

If I recall, -b and -e cannot be the same.  This is the reason for -dump.  It 
might be worth a try to see if trjconv -b 13 -e 14 -dump 14 speeds things up 
any.

-Justin

 Sanku
 
 

-- 

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 regarding replica exchange

[Sanku M]

Hi,

  I am planning to run replica exchange simulation using gromacs 4.0.7 . I have 
read the manual about REMD. Only thing I wanted to know is that how I can 
specify the name of host-machines where I am planning to run the simulations. 

I have 10 different quad-core computers each intra-connected with the other 
each 
running OPENMPI. I want to run 20 replica each using 2 cores in parallel.

So, I was wondering whether I have to create any file containing the names of 
those machines . If so, can someone give an example of format of the file which 
contain those names ? Finally, what keyword I should use in mdrun to specify 
that file for running replica exchange. 

Also, I am not using any PBS for submitting jobs.

Sanku-- 
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Re: [gmx-users] query regarding replica exchange

[Sanku M]

I was wondering if I try to run PBS script in a cluster, how can I get to 
generate the hostfile as I do not know in advance which machines will be 
allocated .





From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wed, May 25, 2011 7:16:44 PM
Subject: Re: [gmx-users] query regarding replica exchange

On 26/05/2011 8:50 AM, Joshua L. Phillips wrote:
 You will need a file formatted like the following:

 node0 slots=4 max_slots=4
 node1 slots=4 max_slots=4
 ...
 node9 slots=4 max_slots=4

 You will then need to use the -hostfile option to supply the filename to
 either mpiexec or mpirun (not mdrun).

Indeed. Details will vary with the nature of the MPI installation -  but 
it's an MPI issue, not a GROMACS issue. The only relevant detail is that 
you wish every pair of cores assigned to a replica to be on the same 
machine. The above approach will generally achieve that.

Mark

 -- Josh

 On Wed, 2011-05-25 at 11:50 -0700, Sanku M wrote:
 Hi,


I am planning to run replica exchange simulation using gromacs
 4.0.7 . I have read the manual about REMD. Only thing I wanted to know
 is that how I can specify the name of host-machines where I am
 planning to run the simulations.


 I have 10 different quad-core computers each intra-connected with the
 other each running OPENMPI. I want to run 20 replica each using 2
 cores in parallel.


 So, I was wondering whether I have to create any file containing the
 names of those machines . If so, can someone give an example of format
 of the file which contain those names ? Finally, what keyword I should
 use in mdrun to specify that file for running replica exchange.


 Also, I am not using any PBS for submitting jobs.


 Sanku








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[gmx-users] Restarting replica exchange simulation

[Sanku M]

Hi,
  I was running a replica exchange simulation in a PBS queue which was killed 
as 
my simulation crossed the maximum time limit. I was planning to restart the 
simulation. I am using gromacs 4.0.7 
 I was wondering what should be the command line arguement  for the multiple 
.cpt file for restarting the replica exchange simulation. 
My .cpt files are named like state0.cpt,state1.cpt,state2.cpt etc  while my 
.tpr 
file topol_0.tpr,topol_1.tpr etc.  Should I put state*.cpt   for mentioning the 
multiple .cpt files ?
i.e 
Will it be something like :
   mpirun -np $NPROCS ~/UTIL_icc/gromacs-4.0.7/bin/mdrun_4mpi  -cpi state*.cpt 
-s topol_.tpr -v -multi 40 -replex 1000  log_replex_test
 
Thanks
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[gmx-users] Dreiding force field in Gromacs ?

[Sanku M]

Hi,

  I was wondering whether Gromacs can be used to perform simulation using 
Dreiding force field developed by Goddard and co-workers ( J.Phys.Chem. 
,94,8897,1990). If someone can share some experience in porting this force 
field 
in gromacs, that will be very helpful.

Sanku-- 
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[gmx-users] g_rdf: how to change grid spacing for structure factor

[Sanku M]

Hi,
  I am using gromacs_4.0.7 to calculate the Scattering Intensity as a function 
of scattering vectors(q) using g_rdf -sq command .
But, I found that there is no way that one can increase/decrease the grid 
spacing  for structure factor calculation. I tried using -bin option , but that 
does not change anything as that only works for changing bin-width for Radial 
distribution function calculation. 
If some one can point me out any way out of changing the grid spacing for 
structure factor, that will be very helpful.

Sanku-- 
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[gmx-users] g_rdf problem

[Sanku M]

Hi,
  I am using gromacs_4.0.7 to calculate the Scattering Intensity as a function 
of scattering vectors(q) using g_rdf -sq command .
But, I found that there is no way that one can increase/decrease the grid 
spacing  for structure factor calculation. I tried using -bin option , but that 
does not change anything as that only works for changing bin-width for Radial 
distribution functioncalculation. 
If some one can point me out any way out of changing the grid spacing 
for structure factor, that will be very helpful.

Sanku-- 
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[gmx-users] Transition path sampling

[Sanku M]

Hi ,
   I was wondering whether current GROMACS versions can perform transition path 
sampling to study rare events ?
Sanku
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[gmx-users] helix dihedral constraint

[Sanku M]

Hi,
 I wanted to run an atomistic  simulation where I would like to constrain 
helicity of a helical peptide( i.e the initial configuration is an ideal helix) 
. I was wondering whether there is a way to constrain the helix dihedral angles 
in Gromacs. Also, if there is any other option to keep the molecule helix, 
please let me know.
 I am using gromacs4.0.7
Thanks
Sanku-- 
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[gmx-users] dipole-dipole interaction energy

[Sanku M]

Hi,
  I am trying to calculate the dipole-dipole interaction energy of two charged 
molecules. But, I was looking for a method/formula to do that. I have the .xtc 
file from which I can calculate the dipole moment of each of the molecule using 
g_dipole . But, then how will I calculate the dipole-dipole interaction energy 
among them ?
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[gmx-users] trjorder and index

[Sanku M]

Hi,
  I am trying to use trjorder command to generate a sorted trajectory where all 
the water molecules are certain distance away. I can use the trjorder command 
to 
generate the sorted trajectory where all waters are sorted based on distance 
but 
I am looking for method for creating a index file which will have  only those 
water molecules which are ,say 0.4 nm away from protein. So far, I could not 
find any way in trjorder which can give me an index file containing the water 
molecules certain distance away. -nshell option in trjorder only gives the 
number of water molecules within a distance but does not specify their indices.

 Also, since the water molecules are always fluctuating, the number of water 
within a certain distance and their indexing will change all the time.
So, I was wondering whether you can suggest a way where I can create an index 
file from the sorted trajectory so as to have only those waters which are 
certain distance away. I mean : is there any way in make_ndx tool , where one 
can do it using certain keywords. 

Any help will be really appreciated.
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[gmx-users] Replica exchange and wham

[Sanku M]

Hi,
Occasionally I hear that one need to use WHAM( weighed histogram analysis) 
method in collaboration with  Temperature-Replica exchange simulation. But, I 
was not understanding why one need to use WHAM with temperature-remd 
simulation. 
Can someone explain me ?
Does one need to use any sorts of WHAM to analyze the trajectory obtained from 
T-REMD simulation of Gromacs ?
 The fact is that I am trying some replica-exchange simulation in gromacs and I 
get all the trajectory which I believed corresponds to each individual 
temperature. I was wondering whether someone can explain me whether I need to 
some WHAM-like post processing to get the data.
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[gmx-users] residence time calculation

[Sanku M]

Hi ,
I am planning to calculate the residence time of a counter-ion near the 
charged head group of surfactant. I was wondering whether some one can suggest 
how one can calculate residence time in gromacs?
Thanks
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Re: [gmx-users] residence time calculation

[Sanku M]

Hi,
  I looked into the mailing list and I found that there is a method where one 
uses g_hbond -contact -ac option to calculate the autocorrelation function of a 
contact pair and then integrate the autocorrelation function to get the 
correlation time. I guess the correlation time is the residence time. Is it ? 
Sanku




From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tue, July 12, 2011 9:13:20 PM
Subject: Re: [gmx-users] residence time calculation



Sanku M wrote:
 Hi ,
 I am planning to calculate the residence time of a counter-ion near the 
charged head group of surfactant. I was wondering whether some one can suggest 
how one can calculate residence time in gromacs?

A similar topic was just discussed a few hours ago.  Please check the archive.

-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] XTC I/O error in replica exchange

[Sanku M]

Hi,
  I am running a replica exchange simulation using 64 replicas ( using 
gromacs4.0.7) in a super computer using 2 nodes ( each having 32 processors). 
But, what happens is that after running for a day or so, the simulation crashes 
with error like 'XTC error, may be you are out of quota'. But, I have checked 
the disc space with the sysadmin and there is no lack of disc space. I am not 
sure what is causing this problem. Any help will be appreciated. 
Sanku-- 
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[gmx-users] g_dist with multiple chains of molecules

[Sanku M]

Hi,
  I am running a simulation where I have 100 chains of molecule in a box . I am 
trying to calculate the distance between two particular atoms ( present in each 
molecule)  averaged over all the chains of molecule. i.e If I have atom C1 and 
C2 in each of the molecule-chain, I want to calculate the distance between C1 
and C2 atom in each chain and average over them.
I was trying to use gromacs 4.0.7  g_dist tool . For that, I first created two 
 index-groups  of all C1 and C2 . But. I realized that g_dist will give me 
actually the distance between center of mass of all C1 and center of mass of 
all 
C2 which is NOT certainly I was looking for.
 So, I was wondering whether there is any other tool which can split the entire 
index group by deviding it by total number of chains and then calculate each 
individual distances for each chain and then do an average over them.


An analogous tool exists for g_gyrate where where one can use -nmol option to 
split the entire index accordingly and calculate the radius of gyration 
averaged 
over all the molecules. I was looking for something for calculating distances 
between two atoms for many chain molecules.

I looked at the mailing list but I could not find any solutions for these. Any 
help will be appreciated.

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[gmx-users] Poisson-Boltzmann free energy in gromacs?

[Sanku M]

Hi,
  I was wondering whether, in gromacs,  there is any way of calculating the 
electrostatic free energy using poisson Boltzmann equation. 
Sanku-- 
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[gmx-users] How to read XTC file in fortran code

[Sanku M]

Hi,
 I was planning to do some analysis by reading in a XTC file using Fortran code 
. I was wondering what is the best possible option I can have .
Sanku-- 
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[gmx-users] query on Free energy perturbation

[Sanku M]

Hi,
  I was planning to use Thermodynamic integration to calculate solvation free 
energy of a molecule in a solvent. I was following Justin Lemkul's online 
tutorial.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html

 
. I found that 
   a) a sd integrator is used in stead of usual md integrator ( Leap-Frog 
integrator). I was wondering whether is it a specific recommendation for 
thermodynamic integration to use stochastic integrator ?
  b) I also found  DispCorr  = EnerPres was also used to Apply 
long range dispersion corrections for Energy and Pressure . Is it also a 
recommendation to use with thermodyanmic integration technique ?
Thanks
Jagannath-- 
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[gmx-users] umbrella sampling using replica exchange

[Sanku M]

Hi,
 I was wondering whether in gromacs 4, one can use replica exchange simulation 
in combination with umbrella sampling.
Thanks
Sanku-- 
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[gmx-users] Problem with temperature and stochastic dynamics in FEP

[Sanku M]

Hi,
  I am trying to calculate the solvation free energy using thermodynamic 
integration(TI) method . I am using gromacs 4.0.7 . But, I am having a problem 
in getting accurate average temperature .
The following is what I did:
   I found that when doing TI, grompp recommends using 'sd' ( stochastic 
dynamics ) as integrator ( provides an warning that for decoupled system, it is 
better to use sd in stead of md ).
Also I went through Justin Lemkul's tutorial which also recommends using 'sd' 
for TI method.   So, I tried to use sd integrator. 

I wanted to run NVT simulation at 300 K.
I also found from manual and also from Justin's website on FEP, sd integrator 
implicitly controls temperature and so there is no need to specify a 
thermostat. 
So, I did not specify any thermostat ( I wrote tcoupl = No ). But, 
unfortunately, I found that after a long simulation  , the average temperature 
actually goes to 303 K in stead of 300 K( the desired temperature). This 
happened for all Lambda values where the average temperature turned out to be 
303 K. The .mdp file is pasted at the end of the email and I felt I am using 
reasonable cutoffs and PME as electrostatics.

Here is the output from g_energy command to get the temperature. 
 
 Statistics over 401 steps [ 0. thru 8000.0005 ps ], 1 data sets
All averages are exact over 401 steps

Energy  Average   RMSD Fluct.  Drift  Tot-Drift
---
Temperature 303.3334.780844.78082 5.46937e-06   0.043755
Heat Capacity Cv:  12.4764 J/mol K (factor = 0.00024841)


I tried three  further tests:
a) I removed tcoupl = No option . But, it is giving same 303K as average 
temperature when using sd.

a)  I tried to specify the Nose-Hoover thermostat along with sd. But still, I 
found that when using sd, the average  temperature is going to 303 K in stead 
of 
300 K.

c)  Finally, I tried to overlook grompp warning and went ahead and used 'md' 
along with Nose-Hoover thermostat. This time I found the right average 
temperature 300 K is being achieved.B
But, I understand that for a decoupled system like here, I need to use a method 
like stochastic dynamics. 

 But , I was wondering why it is reaching 303 K in stead of 300 K when using sd 
 but 300K is achieved when using md. I looked at the mailing list where people 
had issues with sd and temperature control. But, I could not find a good 
solution. So, any help on the right protocol will be really appreciated.


Here is my .mdp file.

; RUN CONTROL PARAMETERS
integrator   = sd
; Start time and timestep in ps
tinit= 0.0
dt   = 0.002
nsteps   = 400
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files separate)
simulation_part  = 1
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=
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric  = 0
ld-seed  = 1993



; OUTPUT CONTROL OPTIONS
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 1
nstvout  = 1
nstfout  = 0
; Output frequency for energies to log file and energy file
nstlog   = 1000
nstenergy= 10
; Output frequency and precision for xtc file
nstxtcout= 1000
xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps   =

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 10
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1.4

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = pme
rcoulomb-switch  = 0
rcoulomb = 1.4
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1
; Method for doing Van der Waals
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = shift
; cut-off lengths
rvdw-switch  = 1.0
rvdw = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; 

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

[Sanku M]

Hi Justin,
  I first performed two minimization using steep and l-bfgs as the method on 
the 
solvated system for each lambda. Then I ran a 500ps NVT simulation on minimized 
system ( for each lambda) where essentially same .mdp file was used except the 
following change: 

   gen-vel  = yes gen-temp= 280
 gen-seed= -1


So, essentially, I heated the minimized system up from 280 K with ref_t 300K 
using sd integrator. But, here also I found the average temperature goes to 303 
K( instead of 300 K) .
One thing I don't understand that why using md as integrator gives the desired 
average temperature( when using Nose-Hoover thermostat) while the sd integrator 
does not.
Any further suggestion will be appreciated.

Jagannath



From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tue, August 2, 2011 8:08:20 PM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP



Sanku M wrote:
 Hi,
   I am trying to calculate the solvation free energy using thermodynamic 
integration(TI) method . I am using gromacs 4.0.7 . But, I am having a problem 
in getting accurate average temperature .
 The following is what I did:
I found that when doing TI, grompp recommends using 'sd' ( stochastic 
dynamics ) as integrator ( provides an warning that for decoupled system, it 
is 
better to use sd in stead of md ).
 Also I went through Justin Lemkul's tutorial which also recommends using 'sd' 
for TI method.   So, I tried to use sd integrator. 


The tutorial uses BAR for calculation free energy, not TI.  Though the 
protocols 
are similar, there is a difference, FYI.

 I wanted to run NVT simulation at 300 K.
 I also found from manual and also from Justin's website on FEP, sd integrator 
implicitly controls temperature and so there is no need to specify a 
thermostat. 
So, I did not specify any thermostat ( I wrote tcoupl = No ). But, 
unfortunately, I found that after a long simulation  , the average temperature 
actually goes to 303 K in stead of 300 K( the desired temperature). This 
happened for all Lambda values where the average temperature turned out to be 
303 K. The .mdp file is pasted at the end of the email and I felt I am using 
reasonable cutoffs and PME as electrostatics.
 
 Here is the output from g_energy command to get the temperature.   Statistics 
over 401 steps [ 0. thru 8000.0005 ps ], 1 data sets
 All averages are exact over 401 steps
 
 Energy  Average   RMSD Fluct.  Drift  
Tot-Drift
 
---
 Temperature 303.3334.780844.78082 5.46937e-06   
0.043755
 Heat Capacity Cv:  12.4764 J/mol K (factor = 0.00024841)
 
 
 I tried three  further tests:
 a) I removed tcoupl = No option . But, it is giving same 303K as average 
temperature when using sd.
 
 a)  I tried to specify the Nose-Hoover thermostat along with sd. But still, I 
found that when using sd, the average  temperature is going to 303 K in stead 
of 
300 K.
 

From the manual description of the sd integrator: The parameter tcoupl is 
ignored.  This explains (a) and (b).

 c)  Finally, I tried to overlook grompp warning and went ahead and used 'md' 
along with Nose-Hoover thermostat. This time I found the right average 
temperature 300 K is being achieved.B
 But, I understand that for a decoupled system like here, I need to use a 
 method 
like stochastic dynamics. 

  But , I was wondering why it is reaching 303 K in stead of 300 K when using 
sd  but 300K is achieved when using md. I looked at the mailing list where 
people had issues with sd and temperature control. But, I could not find a 
good 
solution. So, any help on the right protocol will be really appreciated.
 

What type of equilibration did you do prior to the data collection?  If your 
system isn't sampling the desired ensemble, then you shouldn't proceed.

-Justin

 
 Here is my .mdp file.
 
 ; RUN CONTROL PARAMETERS
 integrator   = sd
 ; Start time and timestep in ps
 tinit= 0.0
 dt   = 0.002
 nsteps   = 400
 ; For exact run continuation or redoing part of a run
 ; Part index is updated automatically on checkpointing (keeps files separate)
 simulation_part  = 1
 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=
 ; LANGEVIN DYNAMICS OPTIONS
 ; Friction coefficient (amu/ps) and random seed
 bd-fric  = 0
 ld-seed  = 1993
 
 
 
 ; OUTPUT CONTROL OPTIONS
 ; OUTPUT CONTROL OPTIONS
 ; Output frequency for coords (x), velocities (v) and forces (f)
 nstxout

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

[Sanku M]

Hi Justin,
  So, do you suggest that after minimization, I should generate the velocity at 
300K instead ?
i.,e for equilibration,should following the set-up?

gen-vel  = yes
  gen-temp= 300
  gen-seed= -1




From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tue, August 2, 2011 8:26:16 PM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP



Justin A. Lemkul wrote:
 
 
 Sanku M wrote:
 Hi Justin,
   I first performed two minimization using steep and l-bfgs as the method on 
the solvated system for each lambda. Then I ran a 500ps NVT simulation on 
minimized system ( for each lambda) where essentially same .mdp file was used 
except the following change:
gen-vel  = yes
  gen-temp= 280
  gen-seed= -1
 
 So, essentially, I heated the minimized system up from 280 K with ref_t 300K 
using sd integrator. But, here also I found the average temperature goes to 
303 
K( instead of 300 K) .
 
 Unless you did simulated annealing in between, you didn't heat the system, 
 you 
suddenly jolted the temperature, which is probably not stable.  Maybe the 
integrator/Langevin thermostat does not react well to these conditions. 
Equilibrate under the conditions you wish to collect data.  Your data 
collection 
uses NPT, so running NVT at a different temperature and suddenly changing the 
temperature and introducing pressure coupling is not an appropriate procedure. 
If nothing else, your data will be unreliable, even if your temperature was 
correct.
 

Sorry, misread the previous .mdp settings.  You're still using NVT, but the 
point about the temperature is still valid here.

-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] Problem with temperature and stochastic dynamics in FEP

[Sanku M]

OKK, But, before, I have tried using md as integrator where I start the initial 
velocity as 280K ( which makes sense as the minimized configuration is 
essentially at low temperature) and have used Nose-hoover at 300K and I never 
had problem in getting the desired 300K after running a short NVT simulation as 
equilabration.
The problem arises when sd integrator is used.
In fact, I  just tried to generate the initial velocity at 300K along with sd 
integrator. I got the 303 K as average temperature again. The same simulation 
using md integrator always gives rise to 300K as average temperature( when used 
in conjunction with Nose-Hoover ) , even if I generate velocity at 280 K or 
300K 
.

I guess that the initial velocity-generation temperature should not be an issue 
here. The sd integrator in contrast to md integrator may be the problem.






From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tue, August 2, 2011 8:40:21 PM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP



Sanku M wrote:
 Hi Justin,
   So, do you suggest that after minimization, I should generate the velocity 
 at 
300K instead ?
 i.,e for equilibration,should following the set-up?
 

You should always equilibrate under the desired conditions.  Never make sudden 
changes, or else you're going to damage the stability of the system.

-Justin

 gen-vel  = yes
   gen-temp= 300
   gen-seed= -1
 
 
 *From:* Justin A. Lemkul jalem...@vt.edu
 *To:* Discussion list for GROMACS users gmx-users@gromacs.org
 *Sent:* Tue, August 2, 2011 8:26:16 PM
 *Subject:* Re: [gmx-users] Problem with temperature and stochastic dynamics 
 in 
FEP
 
 
 
 Justin A. Lemkul wrote:
  
  
   Sanku M wrote:
   Hi Justin,
I first performed two minimization using steep and l-bfgs as the method 
 on 
the solvated system for each lambda. Then I ran a 500ps NVT simulation on 
minimized system ( for each lambda) where essentially same .mdp file was used 
except the following change:
  gen-vel  = yes
gen-temp= 280
gen-seed = -1
  
   So, essentially, I heated the minimized system up from 280 K with ref_t 
300K using sd integrator. But, here also I found the average temperature goes 
to 
303 K( instead of 300 K) .
  
   Unless you did simulated annealing in between, you didn't heat the system, 
you suddenly jolted the temperature, which is probably not stable.  Maybe the 
integrator/Langevin thermostat does not react well to these conditions. 
Equilibrate under the conditions you wish to collect data.  Your data 
collection 
uses NPT, so running NVT at a different temperature and suddenly changing the 
temperature and introducing pressure coupling is not an appropriate procedure. 
If nothing else, your data will be unreliable, even if your temperature was 
correct.
  
 
 Sorry, misread the previous .mdp settings.  You're still using  NVT, but the 
point about the temperature is still valid here.
 
 -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 
mailto:gmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 Please don't post (un)subscribe requests to the list. Use the www interface 
 or 
send it to gmx-users-requ...@gromacs.org 
mailto:gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 

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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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 
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 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

[Sanku M]

Hi Justin,
   I did calculate the average temperature using last 2 ns of the 8ns data. It 
is still same 303K. 





From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tue, August 2, 2011 9:55:40 PM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP



Sanku M wrote:
 OKK, But, before, I have tried using md as integrator where I start the 
 initial 
velocity as 280K ( which makes sense as the minimized configuration is 
essentially at low temperature) and have used Nose-hoover at 300K and I never 
had problem in getting the desired 300K after running a short NVT simulation 
as 
equilabration.
 The problem arises when sd integrator is used.
 In fact, I  just tried to generate the initial velocity at 300K along with sd 
integrator. I got the 303 K as average temperature again. The same simulation 
using md integrator always gives rise to 300K as average temperature( when 
used 
in conjunction with Nose-Hoover ) , even if I generate velocity at 280 K or 
300K 
.
 
 I guess that the initial velocity-generation temperature should not be an 
 issue 
here. The sd integrator in contrast to md integrator may be the problem.
 
 

I have never had such a problem when using sd.  I can always achieve the target 
temperature within 0.5 K, if not exactly, so I do not believe there is an 
inherent problem with sd.  Your first post indicated that your statistics were 
collected over the entire timeframe, which will not be correct for reasons I 
have already described.  The initial frames will represent unequilibrated data 
that may skew the averages.  What if you analyze only the last half of the 
time?  The last 1 ns?

-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
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Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

[Sanku M]

Finally, I achieved the desired 300K average temperature using sd 
integrator 
. I had to reduce the time step from 0.002 ps to 0.001 ps and then running the 
NVT could produce 300K as average temperature.
Still Not sure why md integrator still could 300K average temperature using 
0.002 ps as time-step.




From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tue, August 2, 2011 10:16:17 PM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP



Sanku M wrote:
 Hi Justin,
I did calculate the average temperature using last 2 ns of the 8ns data. 
 It 
is still same 303K. 

 

Going back to the original .mdp file, I can see that you're using some 
incorrect 
settings.  You've set rlist=rvdw even though you're using a shifted potential 
for van der Waals interactions.  Surely grompp should have warned you that this 
would lead to poor energy conservation.  Your solvent is probably heating up as 
a result and leading to the incorrect temperature.

-Justin

 
 *From:* Justin A. Lemkul jalem...@vt.edu
 *To:* Discussion list for GROMACS users gmx-users@gromacs.org
 *Sent:* Tue, August 2, 2011 9:55:40 PM
 *Subject:* Re: [gmx-users] Problem with temperature and stochastic dynamics 
 in 
FEP
 
 
 
 Sanku M wrote:
   OKK, But, before, I have tried using md as integrator where I start the 
initial velocity as 280K ( which makes sense as the minimized configuration is 
essentially at low temperature) and have used Nose-hoover at 300K and I never 
had problem in getting the desired 300K after running a short NVT simulation 
as 
equilabration.
   The problem arises when sd integrator is used.
   In fact, I  just tried to generate the initial velocity at 300K along with 
sd integrator. I got the 303 K as average temperature again. The same 
simulation 
using md integrator always gives rise to 300K as average temperature( when 
used 
in conjunction with Nose-Hoover ) , even if I generate velocity at 280 K or 
300K 
.
  
   I guess that the initial velocity-generation temperature should not be an 
issue here. The sd integrator in contrast to md integrator may be the problem.
  
  
 
 I have never had such a problem when using sd.  I can always achieve the 
 target 
temperature within 0.5 K, if not exactly, so I do not believe there is an 
inherent problem with sd.  Your first post indicated that your statistics were 
collected over the entire timeframe, which will not be correct for reasons I 
have already described.  The initial frames will represent unequilibrated data 
that may skew the averages.  What if you analyze only the last half of the 
time?  The last 1 ns?
 
 -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 
mailto:gmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 Please don't post (un)subscribe requests to the list. Use the www interface 
 or 
send it to gmx-users-requ...@gromacs.org 
mailto:gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 

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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 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 
 
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Ph.D. Candidate
ICTAS Doctoral

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

[Sanku M]

Hi Mark and Justin,
  I did investigate on the rvdw=rlist issue. But, I found even if I make rvdw  
rlist and still keep time step 0.002, the average temperature goes to 303 K.
Only reducing the time step does help ( even if rvdw=rlist) to get average 
temperature to 300K.
Sanku




From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tue, August 2, 2011 11:46:21 PM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

 On 3/08/2011 2:23 PM, Sanku M wrote: 


Finally, I achieved the desired 300K   average temperature using 
 sd 
integrator . I had to reduce the   time step from 0.002 ps to 0.001 ps 
and then running the NVT   could produce 300K as average temperature.
Still Not sure why md integrator still   could 300K average 
temperature 
using 0.002 ps as time-step.
So your integration step was too large to conserve energy. There have been 
two suggestions made about why that might be true. Have you investigated 
them?

Mark






From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tue,   August 2, 2011 10:16:17 PM
Subject: Re: [gmx-users] Problem with temperature and stochastic   
dynamics in FEP



Sanku M wrote:
 Hi Justin,
I did calculate the average temperature using last 2 ns of 
 the 
8ns data. It is still same 303K. 

 

Going back to the original .mdp file, I can see that you're using 
some incorrect settings.  You've set rlist=rvdw even though you're 
using a shifted potential for van der Waals interactions.  Surely 
grompp should have warned you that this would lead to poor energy 
conservation.  Your solvent is probably heating up as a result and 
leading to the incorrect temperature.

-Justin

 

 *From:* Justin A. Lemkul jalem...@vt.edu
 *To:* Discussion list for GROMACS users gmx-users@gromacs.org
 *Sent:* Tue, August 2, 2011 9:55:40 PM
 *Subject:* Re: [gmx-users] Problem with temperature and 
 stochastic 
dynamics in FEP
 
 
 
 Sanku M wrote:
   OKK, But, before, I have tried using md as integrator where I 
start the initial velocity as 280K ( which makes sense as the 
minimized configuration is essentially at low temperature) and 
have 
used Nose-hoover at 300K and I never had problem in getting the 
desired 300K after running a short NVT simulation as 
equilabration.
   The problem arises when sd integrator is used.
   In fact, I  just tried to generate the initial velocity at 
 300K 
along with sd integrator. I got the 303 K as average temperature 
again. The same simulation using md integrator always gives rise 
to 
300K as average temperature( when used in conjunction with 
Nose-Hoover ) , even if I generate velocity at 280 K or 300K .
  
   I guess that the initial velocity-generation temperature 
 should 
not be an issue here. The sd integrator in contrast to md 
integrator 
may be the problem.
  
  
 
 I have never had such a problem when using sd.  I can always 
achieve the target temperature within 0.5 K, if not exactly, so I 
do 
not believe there is an inherent problem with sd.  Your first 
post 
indicated that your statistics were collected over the entire 
timeframe, which will not be correct for reasons I have already 
described.  The initial frames will represent unequilibrated data 
that may skew the averages.  What if you analyze only the last 
half 
of the time?  The last 1 ns?
 
 -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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-- 

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

Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

[Sanku M]

Yes. I did check the tau_t issue. I used tau_t=2ps as recommended in the manual.
Again here, the simulation with 0.002 ps step gives rise to 303K. But, from now 
on, as per your( and Justin's) recommendation, I am going to use the tau_t=2ps 
and rvdwrlist in conjunction with 0.001 ps time step when using sd integrator 
from my production/equilibration run for all lambda.




From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wed, August 3, 2011 11:00:30 AM
Subject: Re: [gmx-users] Problem with temperature and stochastic dynamics in FEP

 On 4/08/2011 1:51 AM, Sanku M wrote: 
Hi Mark and Justin,
  I did investigate on the rvdw=rlist issue. But, I found   even if I 
make rvdw  rlist and still keep time step 0.002,   the average 
temperature goes to 303 K.
Only reducing the time step does help ( even if rvdw=rlist)   to get 
average temperature to 300K.
... and the tau_t issue I mentioned?

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[gmx-users] possible bug in structure factor calculation in g_rdf?

[Sanku M]

Hi,
   I was using gromacs 4.0.7 to calculate the scattering intensity of polymer 
solvated in a solvent. But, I found a discrepancy in the normalization of the 
calculation when considering only a subset
  of  the entire system ( e.g . only solute from the entire solution) :
This is what I found:

 I  first tried to calculate the scattering intensity of  *only* the polymer ( 
i.e the solute) using trajectory file of the entire solution and .tpr file of 
the entire solution using an index file as shown below

g_rdf_4mpi -s topol -f traj -noxvgr -n -sq sq_polymer_only   EOF
 6
 EOF
( Here index-group 6 is the entire polymer).

But, then I  generated  a .tpr file *only* for the solute ( i.e no solvent) and 
used trjconv to generate the .xtc file *only* for the solute 

trjconv_4mpi -s topol.tpr -f traj.xtc -n index.ndx -o traj_polymer_only.xtc


Now, If I try to calculate the scattering intensity, this time using newly 
generated .xtc file *only* containing the solute and the new .tpr file *only* 
containing the solute as follows:
g_rdf_4mpi -s topol_polymer_only.tpr -f traj_polymer_only.xtc -noxvgr  -sq 
sq_polymer_only1 


I get much higher scattering intensity compared to the earlier case ( where  
trajectory of the entire solution was used and a index file was provided to 
consider the solute only for calculation purpose), however the peak position is 
same for both cases. I think, possibly, there might be a bug which does the 
normalization for the entire solution in stead of the subset of the system if 
asked to. 
Any help in clarifying it will be helpful.


Sanku-- 
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[gmx-users] Hamiltonian replica exchange ?

[Sanku M]

Hi,
   I was wondering whether hamiltonian replica exchange simulation has been 
implemented in latest version of  gromacs . Or, is there any other way of 
performing the hamiltonian replica exchange using some variants of 
lambda-dynamics ?
Sanku-- 
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[gmx-users] Hamiltonian replica exchange?

[Sanku M]

Hi,
   I was wondering whether hamiltonian replica exchange simulation has been 
implemented in latest version of  gromacs . Or, is there any other way of 
performing the hamiltonian replica exchange using some variants of 
lambda-dynamics ?
Sanku-- 
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[gmx-users] Force field for thiocyanate ions

[Sanku M]

Hi,
  Does anyone know about availability of MM pair-wise additive forcefield for 
thiocyanate anion ( SCN- ) , either in CHARMM or OPLS format ?
Sanku-- 
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[gmx-users] problem with g_density -center

[Sanku M]

Hi,

  I am trying to calculate the density profile of  head group of bilayer normal 
to z direction using gromacs 4.0.7. I was trying to center the density profile 
about dx/2.dy/2,0 . But, I am finding problem with using center option. I find 
using -center option does not shift the bilayer to 0. 
The following was my command-lines:
g_density_4mpi -f ../traj_npt -s ../topol -noxvgr -n ../index -b 60 -dens 
number -center -o density_phosphate_symm.xvg


Any help on how to use the center option will be really helpful.

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[gmx-users] BD with Hydrodynamic interactions?

[Sanku M]

Hi,
  I was wondering whether BD simulation integrator in Gromacs also have option 
of including hydrodynamic interactions.
Sanku-- 
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Re: [gmx-users] BD with Hydrodynamic interactions?

[Sanku M]

I did not mean lattice boltzmann by BD.
 By BD I meant Brownian Dynamics. In general, for accuracy in dynamics, one 
uses  hydrodynamic interaction in brownian dynamics simulation. I was wondering 
whether hydrodynamic interaction is invoked in gromacs implementation of 
brownian dynamics simulation.



From: Sanku M msank...@yahoo.com
To: Dommert Florian domm...@icp.uni-stuttgart.de
Sent: Monday, September 26, 2011 6:07 AM
Subject: Re: [gmx-users] BD with Hydrodynamic interactions?


I did not mean lattice boltzmann by BD.
 By BD I meant Brownian Dynamics. In general, for accuracy in dynamics, one 
uses  hydrodynamic interaction in brownian dynamics simulation. I was wondering 
whether hydrodynamic interaction is invoked in gromacs implementation of 
brownian dynamics simulation.



From: Dommert Florian domm...@icp.uni-stuttgart.de
To: Sanku M msank...@yahoo.com; Discussion list for GROMACS users 
gmx-users@gromacs.org
Sent: Monday, September 26, 2011 3:38 AM
Subject: Re: [gmx-users] BD with Hydrodynamic interactions?

On Sun, 2011-09-25 at 14:03 -0700, Sanku M wrote: 
 Hi,
   I was wondering whether BD simulation integrator in Gromacs also
 have option of including hydrodynamic interactions.

Hello,

I do not think, that Gromacs has something like Lattice-Boltzmann
implemented so far. Furthermore you would need a momentum-conserving
method for the calculation of the electrostatic forces, which is not
given with the analytical differentiation of SPME, that conserves only
energy and not momentum.

/Flo

 Sanku
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-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: domm...@icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

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[gmx-users] gromacs installation problem in ibm powerpc system

[Sanku M]

Hi,
  I am having a problem in a cluster which is IBM  PowerPC 970MPs and running 
SUSE linux and it has IBM XL  C  Fortran compliers ( xlf, xlc ).
I was trying to install gromacs 4 there using open-mpi which is already 
installed using ibm compilers.
Here is my configure command:

./configure --prefix=/N/u/tg-jmondal/BigRed/UTIL/gromacs_mod_4_gcc/ 
--enable-mpi --program-suffix=mod_4mpi 
CPPFLAGS=-I/N/soft/linux-sles9-ppc64/fftw3-64-single/include 
LDFLAGS=-L/N/soft/linux-sles9-ppc64/fftw3-64-single/lib/ --without-x CC=xlc 
F77=xlf CXX=xlc++

The configuration part went OK.
But when I wrote make,
it fails with following error:
nb_kernel010_ppc_altivec.h, line 42.44: 1506-275 (S) Unexpected text p_nri 
encountered.
nb_kernel010_ppc_altivec.h, line 42.76: 1506-275 (S) Unexpected text iinr 
encountered.
nb_kernel010_ppc_altivec.h, line 42.102: 1506-275 (S) Unexpected text jindex 
encountered.
nb_kernel010_ppc_altivec.h, line 43.70: 1506-275 (S) Unexpected text jjnr 
encountered.
nb_kernel010_ppc_altivec.h, line 43.98: 1506-275 (S) Unexpected text shift 
encountered.
nb_kernel010_ppc_altivec.h, line 43.124: 1506-275 (S) Unexpected text 
shiftvec encountered.
nb_kernel010_ppc_altivec.h, line 44.70: 1506-275 (S) Unexpected text fshift 
encountered.
nb_kernel010_ppc_altivec.h, line 44.98: 1506-275 (S) Unexpected text gid 
encountered.
nb_kernel010_ppc_altivec.h, line 44.124: 1506-275 (S) Unexpected text pos 
encountered.
nb_kernel010_ppc_altivec.h, line 45.70: 1506-275 (S) Unexpected text faction 
encountered.
nb_kernel010_ppc_altivec.h, line 45.98: 1506-275 (S) Unexpected text charge 
encountered.
nb_kernel010_ppc_altivec.h, line 45.123: 1506-275 (S) Unexpected text p_facel 
encountered.
nb_kernel010_ppc_altivec.h, line 46.69: 1506-275 (S) Unexpected text p_krf 
encountered.
nb_kernel010_ppc_altivec.h, line 46.100: 1506-275 (S) Unexpected text p_crf 
encountered.
nb_kernel010_ppc_altivec.h, line 46.130: 1506-275 (S) Unexpected text Vc 
encountered.
nb_kernel010_ppc_altivec.h, line 47.70: 1506-275 (S) Unexpected text type 
encountered.
nb_kernel010_ppc_altivec.h, line 47.96: 1506-275 (S) Unexpected text p_ntype 
encountered.
nb_kernel010_ppc_altivec.h, line 47.126: 1506-275 (S) Unexpected text 
vdwparam encountered.
nb_kernel010_ppc_altivec.h, line 48.70: 1506-275 (S) Unexpected text Vvdw 
encountered.
nb_kernel010_ppc_altivec.h, line 48.97: 1506-275 (S) Unexpected text 
p_tabscale encountered.
make[5]: *** [nb_kernel010_ppc_altivec.lo] Error 1
make[5]: Leaving directory 
`/N/hd01/tg-jmondal/BigRed/GROMACS_MODIFIED/gromacs-4.0.5_gcc/src/gmxlib/nonbonded/nb_kernel_ppc_altivec'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory 
`/N/hd01/tg-jmondal/BigRed/GROMACS_MODIFIED/gromacs-4.0.5_gcc/src/gmxlib/nonbonded'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory 
`/N/hd01/tg-jmondal/BigRed/GROMACS_MODIFIED/gromacs-4.0.5_gcc/src/gmxlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory 
`/N/hd01/tg-jmondal/BigRed/GROMACS_MODIFIED/gromacs-4.0.5_gcc/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory 
`/N/hd01/tg-jmondal/BigRed/GROMACS_MODIFIED/gromacs-4.0.5_gcc/src'
make: *** [all-recursive] Error 1

Not sure what it means. Any help to resolve the issue will be highly 
appreciated.

Sanku



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[gmx-users] problem in cluster determination : g_clustsize and trjconv -pbc cluster problem

[Sanku M]

Hi,
  I have run a simulation using gromacs 4.0.7 with 50 copies of amphiphilic 
surfactant ( in water) using Martini coarse-grained force-field. Mere 
visualization of trajectories shows that starting with 50 discrete copies, they 
gradually aggregate and finally two well-separated large micelles are formed. 
But, my problem starts in quantifying the cluster-size-distributions . 
Here is what I tried:

1. Initially, I was trying to directly use g_clustsize tools to calculate the 
cluster-size distribution. Here is the command line I used :
   g_clustsize -f traj.xtc -s topol.tpr -mol 

But, It turned out that for all the time-frame, it gives me only single  
cluster having all the molecules , giving a flat line in the time-evolution of 
cluster-size. 
This looks to be wrong as the starting configuration has all the 50 copies of 
surfectatnt well dispersed( at least from visualization) and at the end of the 
simulation the visualization shows two clusters.  Here, since  I am interested 
in the molecules that is part of a cluster , hence I used -mol option.  Without 
this option also, I get almost all the atoms in a single cluster .

Then I tried  
  trjconv  -pbc nojump -f traj.xtc -o traj_nojump.xtc 
 option to take care of periodicity. But, It does not change the result 
g_clustsize_4mpi is giving: it always gives me only 1 cluster. use of -pbc 
whole also gives me same result.

2. I also tried to play with cut-off in g_clustsize . Initially I was using 
default cut-off value ( 0.35 nm) . I tried smaller value but result does not 
change. The most awkward part is that even if I make cut-off distance 0 as 
follows:
   g_clustsize -f traj.xtc -cut 0.0 -s topol -mol 
it still gives me a single cluster !  How can it be possible ? I am pretty sure 
there is something wrong but not able to figure this out. 

3.  Later, I found that in gromacs, there is a description of how to determine 
micelle clusters ( perhaps by Justin Lemkul ? )
   Here is the steps it was recommended : 
1. trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster
2. grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr
3. trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump
But, when I tried the first step  as follows:
trjconv -f traj.xtc -o traj_cluster.gro -dump 0 -pbc cluster,
  it looks like it does not converge and enter an infinite loop: Here is an 
excerpt of the output:
COM:0.000 0.00019.999  iter = 19526  Isq = 12671033.000
COM:0.000 0.000 0.000  iter = 19527  Isq = 12628369.000
COM:0.000 0.00019.999  iter = 19528  Isq = 12671033.000
COM:0.000 0.000 0.000  iter = 19529  Isq = 12628369.000
COM:0.000 0.00019.999  iter = 19530  Isq = 12671033.000
COM:0.000 0.000 0.000  iter = 19531  Isq = 12628369.000
COM:0.000 0.00019.999  iter = 19532  Isq = 12671033.000
COM:0.000 0.000 0.000  iter = 19533  Isq = 12628369.000
COM:0.000 0.00019.999  iter = 19534  Isq = 12671033.000
COM:0.000 0.000 0.000  iter = 19535  Isq = 12628369.000
COM:0.000 0.00019.999  iter = 19536  Isq = 12671033.000
COM:0.000 0.000 0.000  iter = 19537  Isq = 12628369.000
COM:0.000 0.00019.999  iter = 19538  Isq = 12671033.000

I am not sure why I am getting an infinite loop ( looks like lsq is only 
fluctuating between two numbers). I also saw similar kind of report in the 
gromacs mailing list , but no proper solution came to my sight .



Overall, none of the attempts is giving me an appreciable result? 
Can someone help me on this so as to get  right cluster size distribution ? Any 
help will be appreciated.

Thanks
Sanku


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[gmx-users] g_sas for martini coarse-grained particles

[Sanku M]

Hi,
   I am trying to estimate the solvent accessible surface area of  hydrophobic 
tails of  a martini DPPC  lipid bilayer . I was going to use g_sas for that. 
But, I observe that this tool gets the vanderwal radii from vdwradii.dat file. 
But, since the particles in the martini lipids are united-atom types, I was 
wondering what will be a reasonable radius to use for hydrophobic tail 
particles 
of a martini lipid ?

Thanks
Sanku 


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[gmx-users] g_rdf

[Sanku M]

Hi,
  I was trying to use g_rdf to calculate radial distribution function g(r) 
between lipid tails and a peptide close to membrane. What I find is that the 
g(r) never goes to 1 at long distance. It is less than 1 at long distance . 
My general question is : Is it always necessary that g(r) between two particles 
should always be expected to  converge to 1 at long distance ? Or,is  it  true 
that it may be quite possible that g(r) can be smaller than 1 even at longer 
separation for two objects  ?

If someone can clarify my confusion, that will be great.

Sanku


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[gmx-users] Looking for force field for metal oxides

[Sanku M]

Dear gromacs users,
  I was planning to study the interaction of a peptide with a zinc 
oxide ( ZnO) surface.  So, I was  wondering whether there is any forcefield for 
metal oxide especially for Zinc Oxide ( ZnO) in literarure that you can suggest 
that can be used in combination with peptide force-field.
Thanks
Sanku 


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