date:20130425

Likewise, I agreed with what Massimo said.

As an example, I recently did a fairly large set of REMD simulations of a
320-atom disordered peptide with rather more water and many fewer replicas
than you propose. I did so because I expected low barriers and large
maximum diameter (the latter from an implicit-solvent REMD). Even after the
fact, I cannot demonstrate that my decisions were correct (and probably
could not even if I could have produced clearly converged ensembles).

Mark
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Re: [gmx-users] Fwd: Selecting the temperature distribution

2013-04-25 Thread massimo sandal

This hints at an interesting protocol/attempt, at least for a sort of
newbie like me. Can you elaborate? Did they exchange?
On 25 Apr 2013 13:06, Mark Abraham mark.j.abra...@gmail.com wrote:

 Likewise, I agreed with what Massimo said.

 As an example, I recently did a fairly large set of REMD simulations of a
 320-atom disordered peptide with rather more water and many fewer replicas
 than you propose. I did so because I expected low barriers and large
 maximum diameter (the latter from an implicit-solvent REMD). Even after the
 fact, I cannot demonstrate that my decisions were correct (and probably
 could not even if I could have produced clearly converged ensembles).

 Mark
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[gmx-users] Martini with PME, temp two low

Hello all, 

I am trying to test the martini force field with PME for a charged system that 
contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. My 
system works well, if i use the standard shift parameters (correct temp, and 
pressure). But for for the simulation with PME , the temp of the system 
decrease to  290 K. Below my *.mdp parameters for a NPT equil at 298K 


integrator   = md
dt   = 0.020
nsteps   = 1 ; 200ps
nstcomm  = 10
comm-grps=
;refcoord_scaling = com

nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 1000
nstenergy= 100
;nstxtcout= 1000
xtc_precision= 100
;xtc-grps =
energygrps   = AOT W ION OCT

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.

; PME parameters
coulombtype  = PME
rcoulomb = 1.2
rvdw = 1.2
fourierspacing   = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order= 4

tcoupl   = v-rescale
tc-grps  = AOT_W_ION OCT
tau_t= 1.0 1.0
ref_t= 298 298
Pcoupl   = berendsen
Pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

;gen_vel  = no
;gen_temp = 0
;gen_seed = 473529


; MARTINI and CONSTRAINTS
; for ring systems and stiff bonds constraints are defined
; which are best handled using Lincs.

constraints  = none
constraint_algorithm = Lincs
unconstrained_start  = no
lincs_order  = 4
lincs_warnangle  = 3


Results obtained with W/ PME 

   Statistics over 10001 steps using 1001 frames

   Energies (kJ/mol)
   Bond   G96AngleLJ (SR)   Coulomb (SR)   Coul. recip.
1.63789e+041.25195e+03   -4.02093e+05   -8.22079e+03   -4.86843e+04
  PotentialKinetic En.   Total EnergyTemperature Pressure (bar)
   -4.41367e+057.81801e+04   -3.63187e+052.90373e+02   -1.76470e+01
T-AOT_W_ION  T-OCT
2.90629e+022.90357e+02

Results W:o PME

   Energies (kJ/mol)
   Bond   G96AngleLJ (SR)   Coulomb (SR)  Potential
1.60482e+041.24820e+03   -3.34608e+05   -7.33665e+02   -3.18046e+05
Kinetic En.   Total EnergyTemperature Pressure (bar)
8.02685e+04   -2.3e+052.98129e+02   -3.07123e+01

  Box-X  Box-Y  Box-Z
1.52926e+011.52926e+011.52926e+01


T-AOT_W_ION  T-OCT
2.98141e+022.98129e+02


Did I miss something ?


Note that for the moment i do not use the polarizable water model.

Thanks for your help 

Stephane




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[gmx-users] issue in replica exchange


Hi,

I have been recently using the REMD code in gmx-407 and gmx-453 and got a few 
systems crashing for unclear reasons so far. The main tests I made are using 
gmx407 but it is all reproducible with gmx453. The crashing was also reproduced 
(not necessarily at the same time point) on several architectures. 

The system is made of a pair of proteins in a membrane patch and for which the 
relative orientation is controlled by non-native bond/angles/dihedrals to 
perform an umbrella sampling. I use the MARTINI force field but that might not 
be relevant here. 

The crashes occur following exchanges that do not seem to occur the correct way 
and preceded by pressure scaling warnings … indicative of a strong 
destabilisation of the system and eventual explosion. Some information seems to 
be exchanged inaccurately. 

Trying to nail down the problem I got stuck and may be some one can help. I 
placed a pdf file showing plots of bonded/nonbonded energies, temperatures, box 
size etc … around an exchange that does not lead to a crash (here: 
md.chem.rug.nl/~periole/remd-issue.pdf). I plotted stuff every step with the 
temperature colour coded as indicated in the first figure. 

From the figure it appears that the step right after the exchange there is a 
huge jump of Potential energy coming from the LJ(SR) part of it. Although there 
are some small discontinuities in the progression of the bond and angle energy 
around the exchange they seem to fine. The temperature and box size seem to 
respond to it a few step latter while the pressure seems to be affected right 
away but potentially as the Epot will affect the viral and thus the Pressure. 

The other potential clue is that the jumps reduce with the strength of the 
pressure coupling. A 1/2 ps tau_p (Berendsen) will lead to a crash while a 
5/10/20 ps won't. Inspection of the time evolution of the Epot, box … indicates 
that the magnitude of the jumps is reduced and the system ca handle the 
problem. 

One additional info since I first posted the problem (delayed by the file first 
attached but now given with a link) the problem is accentuated when the 
replicas differ in conformation. I am looking at the actual differences as 
you'll read this email.

That is as far as I could go. Any suggestion is welcome.

XAvier.
MD-Group / Univ. of Groningen
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Re: [gmx-users] Martini with PME, temp two low


Did you visualise the system? T in function of time? Epot in function of time? 

As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist = 
1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 if 
nstlist =10.

On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote:

 Hello all, 
 
 I am trying to test the martini force field with PME for a charged system 
 that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. 
 My system works well, if i use the standard shift parameters (correct temp, 
 and pressure). But for for the simulation with PME , the temp of the system 
 decrease to  290 K. Below my *.mdp parameters for a NPT equil at 298K 
 
 
 integrator   = md
 dt   = 0.020
 nsteps   = 1 ; 200ps
 nstcomm  = 10
 comm-grps=
 ;refcoord_scaling = com
 
 nstxout  = 0
 nstvout  = 0
 nstfout  = 0
 nstlog   = 1000
 nstenergy= 100
 ;nstxtcout= 1000
 xtc_precision= 100
 ;xtc-grps =
 energygrps   = AOT W ION OCT
 
 nstlist  = 10
 ns_type  = grid
 pbc  = xyz
 rlist= 1.
 
 ; PME parameters
 coulombtype  = PME
 rcoulomb = 1.2
 rvdw = 1.2
 fourierspacing   = 0.12
 fourier_nx   = 0
 fourier_ny   = 0
 fourier_nz   = 0
 pme_order= 4
 
 tcoupl   = v-rescale
 tc-grps  = AOT_W_ION OCT
 tau_t= 1.0 1.0
 ref_t= 298 298
 Pcoupl   = berendsen
 Pcoupltype   = isotropic
 tau_p= 1.0
 compressibility  = 4.5e-5
 ref_p= 1.0
 
 ;gen_vel  = no
 ;gen_temp = 0
 ;gen_seed = 473529
 
 
 ; MARTINI and CONSTRAINTS
 ; for ring systems and stiff bonds constraints are defined
 ; which are best handled using Lincs.
 
 constraints  = none
 constraint_algorithm = Lincs
 unconstrained_start  = no
 lincs_order  = 4
 lincs_warnangle  = 3
 
 
 Results obtained with W/ PME 
 
   Statistics over 10001 steps using 1001 frames
 
   Energies (kJ/mol)
   Bond   G96AngleLJ (SR)   Coulomb (SR)   Coul. recip.
1.63789e+041.25195e+03   -4.02093e+05   -8.22079e+03   -4.86843e+04
  PotentialKinetic En.   Total EnergyTemperature Pressure (bar)
   -4.41367e+057.81801e+04   -3.63187e+052.90373e+02   -1.76470e+01
T-AOT_W_ION  T-OCT
2.90629e+022.90357e+02
 
 Results W:o PME
 
   Energies (kJ/mol)
   Bond   G96AngleLJ (SR)   Coulomb (SR)  Potential
1.60482e+041.24820e+03   -3.34608e+05   -7.33665e+02   -3.18046e+05
Kinetic En.   Total EnergyTemperature Pressure (bar)
8.02685e+04   -2.3e+052.98129e+02   -3.07123e+01
 
  Box-X  Box-Y  Box-Z
1.52926e+011.52926e+011.52926e+01
 
 
T-AOT_W_ION  T-OCT
2.98141e+022.98129e+02
 
 
 Did I miss something ?
 
 
 Note that for the moment i do not use the polarizable water model.
 
 Thanks for your help 
 
 Stephane
 
 
 
 
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RE: [gmx-users] Differences between 4.5.5 and 4.6.2-dev?

2013-04-25 Thread Berk Hess

Hi,

Twin-range will lead to extra errors, which could be negligible or not.
But the errors should be the same and have the same effects in different 
versions.
I think nothing has changed in the twin-range treatment from 4.5 to 4.6, but I 
am not 100% sure.

Which version with twin-range matches your non twin-range results?

Cheers,

Berk


 Subject: Re: [gmx-users] Differences between 4.5.5 and 4.6.2-dev?
 From: kes...@icp.uni-stuttgart.de
 Date: Thu, 25 Apr 2013 10:38:35 +0200
 To: gmx-users@gromacs.org

 Dear Berk, der GMXers,

 On Apr 23, 2013, at 2:54 PM, Stefan Kesselheim kes...@icp.uni-stuttgart.de 
 wrote:

  The temperature is 300.6, target temperature was 300. That should be fine. 
  I did check weaker fields and weaker thermostat coupling. Everything stayed 
  optimally consistent, within 4.5.5, however incompatible with 4.6.2.
  I'm rerunning with cutoffs=1.4 now. I should get results by tomorrow.

 Now results are there and without twin-range I obtain consistent results 
 between the GMX-versions. I'm now switching on twin-range and rerunning to 
 check if the error does reappear.

 I don't know what would be better: Either I did something wrong in a very 
 stupid way, or ...

 Thanks for your patience
 Stefan

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[gmx-users] Problem with gromacs in Cluster

2013-04-25 Thread Sainitin Donakonda

Hey all,

I recently ran 20ns simulation of protein ligand complex on cluster i used
following script to run simulation

grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
md_test.tpr

mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8

*I saved this as MD.sh And then submited to cluster using following script*

#!/bin/bash
#BSUB -J testgromacs # the job's name/array job
#BSUB -W 120:00   # max. wall clock time in hh:mm
#BSUB -n 8,8  # number of processors Min,Max
#BSUB -o test/output_%J.log # output file
#BSUB -e test/errors_%J.log # error file
#BSUB -M 8192 #Memory limit in MB

echo Started at `date`
echo

cd test

echo Running gromacs test in `pwd`

./MD.sh

echo Finished at `date`


It gave result but when checked files .xtc and created RMSD plots in that
x-axis of this plot i see only 8ns ...but in MD.MDP file i specified 20ns..

Cluster Output says that TERM_RUNLIMIT: job killed after reaching LSF run
time limit.
Exited with exit code 140. i gave maximum cluster time 120 hours..still it
is not sufficient ..

Can any body tell me  how do it split script i such  that i will get all
20ns simulation


Thanks in advance ,

Sainitin
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Re: [gmx-users] Problem with gromacs in Cluster




On 4/25/13 8:28 AM, Sainitin Donakonda wrote:

Hey all,

I recently ran 20ns simulation of protein ligand complex on cluster i used
following script to run simulation

grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
md_test.tpr

mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8

*I saved this as MD.sh And then submited to cluster using following script*

#!/bin/bash
#BSUB -J testgromacs # the job's name/array job
#BSUB -W 120:00   # max. wall clock time in hh:mm
#BSUB -n 8,8  # number of processors Min,Max
#BSUB -o test/output_%J.log # output file
#BSUB -e test/errors_%J.log # error file
#BSUB -M 8192 #Memory limit in MB

echo Started at `date`
echo

cd test

echo Running gromacs test in `pwd`

./MD.sh

echo Finished at `date`


It gave result but when checked files .xtc and created RMSD plots in that
x-axis of this plot i see only 8ns ...but in MD.MDP file i specified 20ns..

Cluster Output says that TERM_RUNLIMIT: job killed after reaching LSF run
time limit.
Exited with exit code 140. i gave maximum cluster time 120 hours..still it
is not sufficient ..

Can any body tell me  how do it split script i such  that i will get all
20ns simulation



You specified a given time limit for the job, and the run exceeded it.  Either 
specify more run time (if allowed) or run your job in shorter intervals that 
will finish within the maximum time limit.


-Justin

--


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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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Re: [gmx-users] Problem with gromacs in Cluster

2013-04-25 Thread Francesco

You can split the simulation in different part (for example 5 ns each),
every time you'll finish one you will extend it adding more time.
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations?highlight=extend

My cluster uses a different script system than yours so I can't help
with it, but basically you have to submit more than 1 job with different
command to execute:

1) first production 
mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8
2) modify the tpr file 
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
3) next X ns 
mpirun -n 8 mdrun -s next.tpr -cpi previous.cpt
4) modify the tpr file 
5) production md
and so on

with qsub you can submit a depending job (-hold_jid) that will run only
when the previous step will finish, in your case there should be a
similar way to do it.

cheers 

Fra

On Thu, 25 Apr 2013, at 12:28 PM, Sainitin Donakonda wrote:
 Hey all,
 
 I recently ran 20ns simulation of protein ligand complex on cluster i
 used
 following script to run simulation
 
 grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
 md_test.tpr
 
 mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8
 
 *I saved this as MD.sh And then submited to cluster using following
 script*
 
 #!/bin/bash
 #BSUB -J testgromacs # the job's name/array job
 #BSUB -W 120:00   # max. wall clock time in hh:mm
 #BSUB -n 8,8  # number of processors Min,Max
 #BSUB -o test/output_%J.log # output file
 #BSUB -e test/errors_%J.log # error file
 #BSUB -M 8192 #Memory limit in MB
 
 echo Started at `date`
 echo
 
 cd test
 
 echo Running gromacs test in `pwd`
 
 ./MD.sh
 
 echo Finished at `date`
 
 
 It gave result but when checked files .xtc and created RMSD plots in that
 x-axis of this plot i see only 8ns ...but in MD.MDP file i specified
 20ns..
 
 Cluster Output says that TERM_RUNLIMIT: job killed after reaching LSF
 run
 time limit.
 Exited with exit code 140. i gave maximum cluster time 120 hours..still
 it
 is not sufficient ..
 
 Can any body tell me  how do it split script i such  that i will get all
 20ns simulation
 
 
 Thanks in advance ,
 
 Sainitin
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  frac...@myopera.com
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Re: [gmx-users] How to fix interfacial tension in NPT

2013-04-25 Thread Souilem Safa

Dear Justin,
Please I want to ask you for the calculation of interfacial tension from
the formula : 1/2 (Pz - (px+py)/2))*Lz
Should I calculate the interfacial tension in every step and take the
average interfacial tension for all the steps or should I take the average
of the presssure tensors from all the steps and calculate the interfacial
tension which will be only one value? Because it gives different values.
Thank you very much


On 22 April 2013 20:48, Souilem Safa safasouil...@gmail.com wrote:

 Dear Justin,
 Thank you very much, that is very kind of you :)



 On 22 April 2013 19:42, Justin Lemkul jalem...@vt.edu wrote:



 On 4/21/13 10:37 PM, Souilem Safa wrote:

 Dear Justin,

 Thanks for your quick reply.
 I used Gromos 96 force field, I found it well reproduce triglycerides
 properties (A. Brasiello et al., 2010). I choose 53a6, I thought it is
 the
 updated one but I'm not sure if it well reproduce the the surface tension
 properties . I found recently one paper simulating
 triglyceride-phospholipid-**water membrane (G. Henneré et al., 2009),
 they
 use united atom force field for simulation.
 Which force field do you think it is better , I'm sorry I have limited
 knowledge about it since I'm just beginner  in MD simulation.


 My advice would be to find a study that has been shown to produce the
 types of data you are interested in, then try to reproduce it exactly.  If
 you can do that, move on to your systems using the same force field.  Only
 then can you sort out whether your results are due to some error that you
 are making (and I did note an important mistake below) or due to the
 limitations of the force field itself.

 -Justin

  On 22 April 2013 10:37, Justin Lemkul jalem...@vt.edu wrote:



 On 4/21/13 9:30 PM, Souilem Safa wrote:

  Dear Justin,
 Thank you for your answer, I'm sorry for delay to reply. Actually I'm
 running a simulation of oil-water interface. I'm using Gromos 53a6
 force
 field which is usually used for triglycerides. after semiisotropic and
 MD
 step I still have around 40 mN.m-1 interfacial tension which is pretty
 far
 from my experimental value. Following is my mdp file for NPT step.
 I would be very grateful if you can help me to solve this issue


 Do you have any reason to believe that 53A6 should reproduce quantities
 like surface tension?  I haven't seen such a demonstration before,
 though I
 admit I haven't actively gone looking.  The cutoffs you are using are
 incorrect for strict use of 53A6; that could be a contributing factor to
 your problems.

 -Justin

   title   = NPT equilibration

 ; Run parameters
 integrator  = md; leap-frog integrator
 nsteps  = 25; 2 *25 = 500 ps
 dt  = 0.002 ; 2 fs
 ; Output control
 nstxout = 500   ; save coordinates every 1 ps
 nstvout = 100   ; save velocities every 0.2 ps
 nstenergy   = 100   ; save energies every 0.2 ps
 nstlog  = 100   ; update log file every 0.2 ps
 ; Bond parameters
 continuation= yes   ; Restarting after NVT
 constraint_algorithm = lincs; holonomic constraints
 constraints = all-bonds ; all bonds (even heavy atom-H bonds)
 constrained
 lincs_iter  = 2 ; accuracy of LINCS
 lincs_order = 2 ; also related to accuracy
 ; Neighborsearching
 ns_type = grid  ; search neighboring grid cells
 nstlist = 5 ; 10 fs
 rlist   = 1.0   ; short-range neighborlist cutoff (in
 nm)
 rcoulomb= 1.0   ; short-range electrostatic cutoff (in
 nm)
 rvdw= 1.0   ; short-range van der Waals cutoff (in
 nm)
 ; Electrostatics
 coulombtype = PME   ; Particle Mesh Ewald for long-range
 electrostatics
 pme_order   = 4 ; cubic interpolation
 fourierspacing  = 0.16  ; grid spacing for FFT
 ; Temperature coupling is on
 tcoupl  = V-rescale ; modified Berendsen thermostat
 tc-grps = SOL TRI   ; two coupling groups - more accurate
 tau_t   = 0.1 0.1   ; time constant, in ps
 ref_t   = 300 300   ; reference temperature, one for each
 group, in K
 ; Pressure coupling is on
 pcoupl  = parrinello-Rahman ; Pressure coupling on in NPT
 pcoupltype  = semiisotropic ; uniform scaling of box
 vectors
 tau_p   = 1.0 1.0   ; time constant, in ps
 ref_p   = 1.0 1.0   ; reference pressure, in bar
 compressibility = 0   4.5e-5; isothermal compressibility x,y axis/z
 axis bar^-1
 refcoord_scaling = com
 ; Periodic boundary conditions
 pbc = xyz   ; 3-D PBC
 ; Dispersion correction
 DispCorr= enerpres  ; account for cut-off vdW scheme
 ; Velocity generation
 gen_vel = no; Velocity generation is off




 On 19 April 2013 03:28, Justin Lemkul jalem...@vt.edu wrote:



 On 4/18/13

[gmx-users] RE : gmx-users Digest, Vol 108, Issue 154

Hello Xavier, 

Thank you for your response. 

 nstlist = 10 and the rlist = 1.0 
My mistake, i did not changes these values when i switched to PME,

I have rerun the simulations for 400 ps in NPT with these changes and plotted 
Epot and Temp vs Time The Epot and Temp values are not stables. The average 
Temp of the system  is better than previously but fluctuate around (294 K) 
instead of 298 K . Note i use gmx4.5.5 to do my calculations.

 I have also visualized my  system at the end of the NPT run, the  na+, water, 
surfactant, octane molecules  form a slab with void

What's wrong ?

Stephane 



--

Message: 5
Date: Thu, 25 Apr 2013 13:34:21 +0200
From: XAvier Periole x.peri...@rug.nl
Subject: Re: [gmx-users] Martini with PME, temp two low
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4632c83b-cd6f-4c92-b887-a1c39dff4...@rug.nl
Content-Type: text/plain; charset=us-ascii


Did you visualise the system? T in function of time? Epot in function of time?

As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist = 
1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 if 
nstlist =10.

On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote:

 Hello all,

 I am trying to test the martini force field with PME for a charged system 
 that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. 
 My system works well, if i use the standard shift parameters (correct temp, 
 and pressure). But for for the simulation with PME , the temp of the system 
 decrease to  290 K. Below my *.mdp parameters for a NPT equil at 298K


 integrator   = md
 dt   = 0.020
 nsteps   = 1 ; 200ps
 nstcomm  = 10
 comm-grps=
 ;refcoord_scaling = com

 nstxout  = 0
 nstvout  = 0
 nstfout  = 0
 nstlog   = 1000
 nstenergy= 100
 ;nstxtcout= 1000
 xtc_precision= 100
 ;xtc-grps =
 energygrps   = AOT W ION OCT

 nstlist  = 10
 ns_type  = grid
 pbc  = xyz
 rlist= 1.

 ; PME parameters
 coulombtype  = PME
 rcoulomb = 1.2
 rvdw = 1.2
 fourierspacing   = 0.12
 fourier_nx   = 0
 fourier_ny   = 0
 fourier_nz   = 0
 pme_order= 4

 tcoupl   = v-rescale
 tc-grps  = AOT_W_ION OCT
 tau_t= 1.0 1.0
 ref_t= 298 298
 Pcoupl   = berendsen
 Pcoupltype   = isotropic
 tau_p= 1.0
 compressibility  = 4.5e-5
 ref_p= 1.0

 ;gen_vel  = no
 ;gen_temp = 0
 ;gen_seed = 473529


 ; MARTINI and CONSTRAINTS
 ; for ring systems and stiff bonds constraints are defined
 ; which are best handled using Lincs.

 constraints  = none
 constraint_algorithm = Lincs
 unconstrained_start  = no
 lincs_order  = 4
 lincs_warnangle  = 3


 Results obtained with W/ PME

   Statistics over 10001 steps using 1001 frames

   Energies (kJ/mol)
   Bond   G96AngleLJ (SR)   Coulomb (SR)   Coul. recip.
1.63789e+041.25195e+03   -4.02093e+05   -8.22079e+03   -4.86843e+04
  PotentialKinetic En.   Total EnergyTemperature Pressure (bar)
   -4.41367e+057.81801e+04   -3.63187e+052.90373e+02   -1.76470e+01
T-AOT_W_ION  T-OCT
2.90629e+022.90357e+02

 Results W:o PME

   Energies (kJ/mol)
   Bond   G96AngleLJ (SR)   Coulomb (SR)  Potential
1.60482e+041.24820e+03   -3.34608e+05   -7.33665e+02   -3.18046e+05
Kinetic En.   Total EnergyTemperature Pressure (bar)
8.02685e+04   -2.3e+052.98129e+02   -3.07123e+01

  Box-X  Box-Y  Box-Z
1.52926e+011.52926e+011.52926e+01


T-AOT_W_ION  T-OCT
2.98141e+022.98129e+02


 Did I miss something ?


 Note that for the moment i do not use the polarizable water model.

 Thanks for your help

 Stephane




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Message: 6
Date: Thu, 25 Apr 2013 14:05:51 +0200
From: Berk Hess g...@hotmail.com
Subject: RE: [gmx-users] Differences between 4.5.5 and 4.6.2-dev?
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:

[gmx-users] Doubt about the Gromacs versions

2013-04-25 Thread bipin singh

Hi,

Please let me know which one is the recent version of gromacs (with latest
bugfixes) among the below.
4.5.7 and 4.6.1

And what is the reason behind the update for 4.5.x versions if 4.6.x
versions are already available.

-- 
*---
Thanks and Regards,
Bipin Singh*
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Re: [gmx-users] Martini with PME, temp two low

2013-04-25 Thread Dr. Vitaly Chaban

Hmmm

Aren't the keywords here charged system + PME?


Dr. Vitaly Chaban



On Thu, Apr 25, 2013 at 1:34 PM, XAvier Periole x.peri...@rug.nl wrote:


 Did you visualise the system? T in function of time? Epot in function of
 time?

 As a side note (not relevant for PME) the mix of nstlist = 10 and the
 rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and
 rlist=1.4 if nstlist =10.

 On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 stephane.a...@cea.fr
 wrote:

  Hello all,
 
  I am trying to test the martini force field with PME for a charged
 system that contains na+, water, surfactant, octane molecules at 298K and
 P=0.1MPa. My system works well, if i use the standard shift parameters
 (correct temp, and pressure). But for for the simulation with PME , the
 temp of the system decrease to  290 K. Below my *.mdp parameters for a NPT
 equil at 298K
 
 
  integrator   = md
  dt   = 0.020
  nsteps   = 1 ; 200ps
  nstcomm  = 10
  comm-grps=
  ;refcoord_scaling = com
 
  nstxout  = 0
  nstvout  = 0
  nstfout  = 0
  nstlog   = 1000
  nstenergy= 100
  ;nstxtcout= 1000
  xtc_precision= 100
  ;xtc-grps =
  energygrps   = AOT W ION OCT
 
  nstlist  = 10
  ns_type  = grid
  pbc  = xyz
  rlist= 1.
 
  ; PME parameters
  coulombtype  = PME
  rcoulomb = 1.2
  rvdw = 1.2
  fourierspacing   = 0.12
  fourier_nx   = 0
  fourier_ny   = 0
  fourier_nz   = 0
  pme_order= 4
 
  tcoupl   = v-rescale
  tc-grps  = AOT_W_ION OCT
  tau_t= 1.0 1.0
  ref_t= 298 298
  Pcoupl   = berendsen
  Pcoupltype   = isotropic
  tau_p= 1.0
  compressibility  = 4.5e-5
  ref_p= 1.0
 
  ;gen_vel  = no
  ;gen_temp = 0
  ;gen_seed = 473529
 
 
  ; MARTINI and CONSTRAINTS
  ; for ring systems and stiff bonds constraints are defined
  ; which are best handled using Lincs.
 
  constraints  = none
  constraint_algorithm = Lincs
  unconstrained_start  = no
  lincs_order  = 4
  lincs_warnangle  = 3
 
 
  Results obtained with W/ PME
 
Statistics over 10001 steps using 1001 frames
 
Energies (kJ/mol)
Bond   G96AngleLJ (SR)   Coulomb (SR)   Coul.
 recip.
 1.63789e+041.25195e+03   -4.02093e+05   -8.22079e+03
 -4.86843e+04
   PotentialKinetic En.   Total EnergyTemperature Pressure
 (bar)
-4.41367e+057.81801e+04   -3.63187e+052.90373e+02
 -1.76470e+01
 T-AOT_W_ION  T-OCT
 2.90629e+022.90357e+02
 
  Results W:o PME
 
Energies (kJ/mol)
Bond   G96AngleLJ (SR)   Coulomb (SR)
  Potential
 1.60482e+041.24820e+03   -3.34608e+05   -7.33665e+02
 -3.18046e+05
 Kinetic En.   Total EnergyTemperature Pressure (bar)
 8.02685e+04   -2.3e+052.98129e+02   -3.07123e+01
 
   Box-X  Box-Y  Box-Z
 1.52926e+011.52926e+011.52926e+01
 
 
 T-AOT_W_ION  T-OCT
 2.98141e+022.98129e+02
 
 
  Did I miss something ?
 
 
  Note that for the moment i do not use the polarizable water model.
 
  Thanks for your help
 
  Stephane
 
 
 
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Re: [gmx-users] Problem with gromacs in Cluster

2013-04-25 Thread Richard Broadbent

I generally build a tpr for the whole simulation then submit one job 
using a command such as:


mpirun -n ${NUM_PROCESSORS} mdrun -deffnm ${NAME} -maxh 
${WALL_TIME_IN_HOURS}


copy all the files back at the end of the script if necessary then:

then resubmit it (sending out all the files again if necessary) this 
time using the command


mpirun -n ${NUM_PROCESSORS} mdrun -deffnm ${NAME} -maxh 
${WALL_TIME_IN_HOURS} -cpi


you can then keep resubmitting with that line till the job is finished.

In my case I have a maximum wall clock of 24hrs on some machines so this 
gets used a lot


I also think that 1.6ns/day which is what you seem to be getting is very 
low performance and you might want to consider using more processors. 
Check the log file as the profiling information at the end will indicate 
whether this might be beneficial.


Richard


On 25/04/13 13:58, Francesco wrote:

You can split the simulation in different part (for example 5 ns each),
every time you'll finish one you will extend it adding more time.
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations?highlight=extend

My cluster uses a different script system than yours so I can't help
with it, but basically you have to submit more than 1 job with different
command to execute:

1) first production
mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8
2) modify the tpr file
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
3) next X ns
mpirun -n 8 mdrun -s next.tpr -cpi previous.cpt
4) modify the tpr file
5) production md
and so on

with qsub you can submit a depending job (-hold_jid) that will run only
when the previous step will finish, in your case there should be a
similar way to do it.

cheers

Fra

On Thu, 25 Apr 2013, at 12:28 PM, Sainitin Donakonda wrote:

Hey all,

I recently ran 20ns simulation of protein ligand complex on cluster i
used
following script to run simulation

grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
md_test.tpr

mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8

*I saved this as MD.sh And then submited to cluster using following
script*

#!/bin/bash
#BSUB -J testgromacs # the job's name/array job
#BSUB -W 120:00   # max. wall clock time in hh:mm
#BSUB -n 8,8  # number of processors Min,Max
#BSUB -o test/output_%J.log # output file
#BSUB -e test/errors_%J.log # error file
#BSUB -M 8192 #Memory limit in MB

echo Started at `date`
echo

cd test

echo Running gromacs test in `pwd`

./MD.sh

echo Finished at `date`


It gave result but when checked files .xtc and created RMSD plots in that
x-axis of this plot i see only 8ns ...but in MD.MDP file i specified
20ns..

Cluster Output says that TERM_RUNLIMIT: job killed after reaching LSF
run
time limit.
Exited with exit code 140. i gave maximum cluster time 120 hours..still
it
is not sufficient ..

Can any body tell me  how do it split script i such  that i will get all
20ns simulation


Thanks in advance ,

Sainitin
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Re: [gmx-users] Martini with PME, temp two low

Sorry for the double post, but i forgot to remove the others message. I have 
also added the average values obtained for this run 

Statistics over 20001 steps using 4001 frames

   Energies (kJ/mol)
   Bond   G96AngleLJ (SR)   Coulomb (SR)   Coul. recip.
1.65683e+041.26644e+03   -4.02287e+05   -8.47260e+03   -4.90494e+04
  PotentialKinetic En.   Total EnergyTemperature Pressure (bar)
   -4.41974e+057.91982e+04   -3.62776e+052.94154e+02   -1.80237e+01

  Box-X  Box-Y  Box-Z
1.51316e+011.51316e+011.51316e+01

   Total Virial (kJ/mol)
2.90936e+04   -4.68005e+01   -2.46005e+01
   -4.68005e+012.92687e+04   -2.56235e+01
   -2.46006e+01   -2.56236e+012.64822e+04

   Pressure (bar)
   -2.57341e+015.58858e-011.46893e-01
5.58858e-01   -2.74443e+012.21040e-01
1.46893e-012.21041e-01   -8.92609e-01

   Total Dipole (D)
4.16699e+021.92049e+026.43137e+02

  Epot (kJ/mol)Coul-SR  LJ-SR
AOT-AOT5.26697e+02   -4.94208e+03
  AOT-W0.0e+00   -2.35002e+03
AOT-ION   -9.54002e+03   -1.89339e+03
AOT-OCT0.0e+00   -2.04448e+04
W-W0.0e+00   -3.88078e+02

Stephane

--

Message: 4
Date: Thu, 25 Apr 2013 13:26:32 +
From: ABEL Stephane 175950 stephane.a...@cea.fr
Subject: [gmx-users] RE : gmx-users Digest, Vol 108, Issue 154
To: gmx-users@gromacs.org gmx-users@gromacs.org
Message-ID:
3e39b768bb199548ab18f7289e7534af1a818...@exdag0-b0.intra.cea.fr
Content-Type: text/plain; charset=us-ascii

Hello Xavier,

Thank you for your response.

 nstlist = 10 and the rlist = 1.0
My mistake, i did not changes these values when i switched to PME,

I have rerun the simulations for 400 ps in NPT with these changes and plotted 
Epot and Temp vs Time The Epot and Temp values are not stables. The average 
Temp of the system  is better than previously but fluctuate around (294 K) 
instead of 298 K . Note i use gmx4.5.5 to do my calculations.

 I have also visualized my  system at the end of the NPT run, the  na+, water, 
surfactant, octane molecules  form a slab with void

What's wrong ?

Stephane



--

Message: 5
Date: Thu, 25 Apr 2013 13:34:21 +0200
From: XAvier Periole x.peri...@rug.nl
Subject: Re: [gmx-users] Martini with PME, temp two low
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4632c83b-cd6f-4c92-b887-a1c39dff4...@rug.nl
Content-Type: text/plain; charset=us-ascii


Did you visualise the system? T in function of time? Epot in function of time?

As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist = 
1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 if 
nstlist =10.

On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote:

 Hello all,

 I am trying to test the martini force field with PME for a charged system 
 that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. 
 My system works well, if i use the standard shift parameters (correct temp, 
 and pressure). But for for the simulation with PME , the temp of the system 
 decrease to  290 K. Below my *.mdp parameters for a NPT equil at 298K


 integrator   = md
 dt   = 0.020
 nsteps   = 1 ; 200ps
 nstcomm  = 10
 comm-grps=
 ;refcoord_scaling = com

 nstxout  = 0
 nstvout  = 0
 nstfout  = 0
 nstlog   = 1000
 nstenergy= 100
 ;nstxtcout= 1000
 xtc_precision= 100
 ;xtc-grps =
 energygrps   = AOT W ION OCT

 nstlist  = 10
 ns_type  = grid
 pbc  = xyz
 rlist= 1.

 ; PME parameters
 coulombtype  = PME
 rcoulomb = 1.2
 rvdw = 1.2
 fourierspacing   = 0.12
 fourier_nx   = 0
 fourier_ny   = 0
 fourier_nz   = 0
 pme_order= 4

 tcoupl   = v-rescale
 tc-grps  = AOT_W_ION OCT
 tau_t= 1.0 1.0
 ref_t= 298 298
 Pcoupl   = berendsen
 Pcoupltype   = isotropic
 tau_p= 1.0
 compressibility  = 4.5e-5
 ref_p= 1.0

 ;gen_vel  = no
 ;gen_temp = 0
 ;gen_seed = 473529


 ; MARTINI and CONSTRAINTS
 ; for ring systems and stiff bonds constraints are defined
 ; which are best handled using Lincs.

 constraints  = none
 constraint_algorithm = Lincs
 unconstrained_start  = no
 lincs_order  = 4
 lincs_warnangle  = 3


 Results obtained with W/ PME

   Statistics over 10001 steps using 1001 frames

Re: [gmx-users] Problem with gromacs in Cluster

2013-04-25 Thread Dr. Vitaly Chaban

The salvation is to use:

mdrun -cpi state.cpt


Dr. Vitaly Chaban




On Thu, Apr 25, 2013 at 2:37 PM, Justin Lemkul jalem...@vt.edu wrote:



 Can any body tell me  how do it split script i such  that i will get all
 20ns simulation


 You specified a given time limit for the job, and the run exceeded it.
  Either specify more run time (if allowed) or run your job in shorter
 intervals that will finish within the maximum time limit.

 -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
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Re: [gmx-users] Doubt about the Gromacs versions

2013-04-25 Thread Richard Broadbent

The 4.6.1 release is a more advanced version of gromacs with the latest 
kernels and features (GPU support, verlet cut-offs etc.).


4.5.7 is a maintenance release for those of us who for whatever reason 
wish to keep using the older 4.5.x series release. It mainly adds fixes 
made to the 4.6.x series to the 4.5.x version of the code. I use it as 
most of my calculations were conducted in 4.5.5 so this version allows 
me to use exactly the same setup as I was using before.


If you are starting a new project I would suggest that the 4.6.x series 
is what you should use as it is substantially faster (for a system I'm 
running that contains no water on an Intel sandy-bridge system it is 
more than 50% faster). This series will also probably receive more 
attention in terms of bug fixes and new releases (though I'm not a 
developer so I could be wrong about that).


Richard


On 25/04/13 14:39, bipin singh wrote:

Hi,

Please let me know which one is the recent version of gromacs (with latest
bugfixes) among the below.
4.5.7 and 4.6.1

And what is the reason behind the update for 4.5.x versions if 4.6.x
versions are already available.


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Re: [gmx-users] Martini with PME, temp two low


Well … 400 ps is rather small and you can expect deviations from so short 
simulations if you start from an non-equilibrated system. I am not sure what 
the void is but this indicates that your system might not be equilibrated … 

You can try to decrease the time step and nstlist to see if you the drop of 
temperature is due a flow of energy. 

On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote:

 Hello Xavier, 
 
 Thank you for your response. 
 
 nstlist = 10 and the rlist = 1.0 
 My mistake, i did not changes these values when i switched to PME,
 
 I have rerun the simulations for 400 ps in NPT with these changes and plotted 
 Epot and Temp vs Time The Epot and Temp values are not stables. The average 
 Temp of the system  is better than previously but fluctuate around (294 K) 
 instead of 298 K . Note i use gmx4.5.5 to do my calculations.
 
 I have also visualized my  system at the end of the NPT run, the  na+, water, 
 surfactant, octane molecules  form a slab with void
 
 What's wrong ?
 
 Stephane 
 
 
 
 --
 
 Message: 5
 Date: Thu, 25 Apr 2013 13:34:21 +0200
 From: XAvier Periole x.peri...@rug.nl
 Subject: Re: [gmx-users] Martini with PME, temp two low
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID: 4632c83b-cd6f-4c92-b887-a1c39dff4...@rug.nl
 Content-Type: text/plain; charset=us-ascii
 
 
 Did you visualise the system? T in function of time? Epot in function of time?
 
 As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist = 
 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 
 if nstlist =10.
 
 On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 stephane.a...@cea.fr 
 wrote:
 
 Hello all,
 
 I am trying to test the martini force field with PME for a charged system 
 that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. 
 My system works well, if i use the standard shift parameters (correct temp, 
 and pressure). But for for the simulation with PME , the temp of the system 
 decrease to  290 K. Below my *.mdp parameters for a NPT equil at 298K
 
 
 integrator   = md
 dt   = 0.020
 nsteps   = 1 ; 200ps
 nstcomm  = 10
 comm-grps=
 ;refcoord_scaling = com
 
 nstxout  = 0
 nstvout  = 0
 nstfout  = 0
 nstlog   = 1000
 nstenergy= 100
 ;nstxtcout= 1000
 xtc_precision= 100
 ;xtc-grps =
 energygrps   = AOT W ION OCT
 
 nstlist  = 10
 ns_type  = grid
 pbc  = xyz
 rlist= 1.
 
 ; PME parameters
 coulombtype  = PME
 rcoulomb = 1.2
 rvdw = 1.2
 fourierspacing   = 0.12
 fourier_nx   = 0
 fourier_ny   = 0
 fourier_nz   = 0
 pme_order= 4
 
 tcoupl   = v-rescale
 tc-grps  = AOT_W_ION OCT
 tau_t= 1.0 1.0
 ref_t= 298 298
 Pcoupl   = berendsen
 Pcoupltype   = isotropic
 tau_p= 1.0
 compressibility  = 4.5e-5
 ref_p= 1.0
 
 ;gen_vel  = no
 ;gen_temp = 0
 ;gen_seed = 473529
 
 
 ; MARTINI and CONSTRAINTS
 ; for ring systems and stiff bonds constraints are defined
 ; which are best handled using Lincs.
 
 constraints  = none
 constraint_algorithm = Lincs
 unconstrained_start  = no
 lincs_order  = 4
 lincs_warnangle  = 3
 
 
 Results obtained with W/ PME
 
  Statistics over 10001 steps using 1001 frames
 
  Energies (kJ/mol)
  Bond   G96AngleLJ (SR)   Coulomb (SR)   Coul. recip.
   1.63789e+041.25195e+03   -4.02093e+05   -8.22079e+03   -4.86843e+04
 PotentialKinetic En.   Total EnergyTemperature Pressure (bar)
  -4.41367e+057.81801e+04   -3.63187e+052.90373e+02   -1.76470e+01
   T-AOT_W_ION  T-OCT
   2.90629e+022.90357e+02
 
 Results W:o PME
 
  Energies (kJ/mol)
  Bond   G96AngleLJ (SR)   Coulomb (SR)  Potential
   1.60482e+041.24820e+03   -3.34608e+05   -7.33665e+02   -3.18046e+05
   Kinetic En.   Total EnergyTemperature Pressure (bar)
   8.02685e+04   -2.3e+052.98129e+02   -3.07123e+01
 
 Box-X  Box-Y  Box-Z
   1.52926e+011.52926e+011.52926e+01
 
 
   T-AOT_W_ION  T-OCT
   2.98141e+022.98129e+02
 
 
 Did I miss something ?
 
 
 Note that for the moment i do not use the polarizable water model.
 
 Thanks for your help
 
 Stephane
 
 
 
 
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[gmx-users] sc-coul and sc-r-power

2013-04-25 Thread Magnus Lundborg


Hello,

My simulations crash when using sc-r-power 48, even if I'm running with 
sc-coul = no, couple_lambda0 = vdw-q couple_lambda1 = vdw.


If I'm running couple_lambda0 = vdw and couple_lambda1 = none it works.

The fe config that is causing a crash is:
init_lambda-state = 0
couple-intramol = no
couple_lambda0 = vdw-q
couple_lambda1 = vdw
sc-r-power   = 48
sc-coul = no
vdw-lambdas =  0.0 0.0 0.0 0.0 0.2 0.4 0.6 0.8 1.0
coul-lambdas = 0.0 0.2 0.5 1.0 1.0 1.0 1.0 1.0 1.0
separate_dhdl_file = yes
sc_sigma = 0.3
sc_power = 1.0
couple_moltype = 2-ethoxyethanol
free_energy = yes
sc_alpha = 0.001


If I change it to:
couple_lambda0 = vdw
couple_lambda1 = none

it works without problem and also if I change it to:
couple_lambda0 = vdw-q
couple_lambda1 = vdw
sc-r-power   = 6


Shouldn't sc-r-power be ignored when using sc-coul = no, couple_lambda0 
= vdw-q and couple_lambda1 = vdw? Or have I misunderstood something?


Regards,

Magnus

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[gmx-users] Martini with PME, temp two low

And ? sorry but i do not understand...

Stephane

--

Message: 2
Date: Thu, 25 Apr 2013 15:39:12 +0200
From: Dr. Vitaly Chaban vvcha...@gmail.com
Subject: Re: [gmx-users] Martini with PME, temp two low
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
CAPXdD+bDiuQWG_3eWZ_0yb=aynlaaf08vt46usel4wk_bjg...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1

Hmmm

Aren't the keywords here charged system + PME?

Dr. Vitaly Chaban

On Thu, Apr 25, 2013 at 1:34 PM, XAvier Periole x.peri...@rug.nl wrote:

 Did you visualise the system? T in function of time? Epot in function of
 time?

 As a side note (not relevant for PME) the mix of nstlist = 10 and the
 rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and
 rlist=1.4 if nstlist =10.

 On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 stephane.a...@cea.fr
 wrote:

  Hello all,

  I am trying to test the martini force field with PME for a charged
 system that contains na+, water, surfactant, octane molecules at 298K and
 P=0.1MPa. My system works well, if i use the standard shift parameters
 (correct temp, and pressure). But for for the simulation with PME , the
 temp of the system decrease to  290 K. Below my *.mdp parameters for a NPT
 equil at 298K

  integrator   = md
  dt   = 0.020
  nsteps   = 1 ; 200ps
  nstcomm  = 10
  comm-grps=
  ;refcoord_scaling = com

  nstxout  = 0
  nstvout  = 0
  nstfout  = 0
  nstlog   = 1000
  nstenergy= 100
  ;nstxtcout= 1000
  xtc_precision= 100
  ;xtc-grps =
  energygrps   = AOT W ION OCT

  nstlist  = 10
  ns_type  = grid
  pbc  = xyz
  rlist= 1.

  ; PME parameters
  coulombtype  = PME
  rcoulomb = 1.2
  rvdw = 1.2
  fourierspacing   = 0.12
  fourier_nx   = 0
  fourier_ny   = 0
  fourier_nz   = 0
  pme_order= 4

  tcoupl   = v-rescale
  tc-grps  = AOT_W_ION OCT
  tau_t= 1.0 1.0
  ref_t= 298 298
  Pcoupl   = berendsen
  Pcoupltype   = isotropic
  tau_p= 1.0
  compressibility  = 4.5e-5
  ref_p= 1.0

  ;gen_vel  = no
  ;gen_temp = 0
  ;gen_seed = 473529

  ; MARTINI and CONSTRAINTS
  ; for ring systems and stiff bonds constraints are defined
  ; which are best handled using Lincs.

  constraints  = none
  constraint_algorithm = Lincs
  unconstrained_start  = no
  lincs_order  = 4
  lincs_warnangle  = 3

  Results obtained with W/ PME

Statistics over 10001 steps using 1001 frames

Energies (kJ/mol)
Bond   G96AngleLJ (SR)   Coulomb (SR)   Coul.
 recip.
 1.63789e+041.25195e+03   -4.02093e+05   -8.22079e+03
 -4.86843e+04
   PotentialKinetic En.   Total EnergyTemperature Pressure
 (bar)
-4.41367e+057.81801e+04   -3.63187e+052.90373e+02
 -1.76470e+01
 T-AOT_W_ION  T-OCT
 2.90629e+022.90357e+02

  Results W:o PME

Energies (kJ/mol)
Bond   G96AngleLJ (SR)   Coulomb (SR)
  Potential
 1.60482e+041.24820e+03   -3.34608e+05   -7.33665e+02
 -3.18046e+05
 Kinetic En.   Total EnergyTemperature Pressure (bar)
 8.02685e+04   -2.3e+052.98129e+02   -3.07123e+01

   Box-X  Box-Y  Box-Z
 1.52926e+011.52926e+011.52926e+01

 T-AOT_W_ION  T-OCT
 2.98141e+022.98129e+02

  Did I miss something ?

  Note that for the moment i do not use the polarizable water model.

  Thanks for your help

  Stephane

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Re: [gmx-users] Martini with PME, temp two low

2013-04-25 Thread Dr. Vitaly Chaban

PME should NOT be used with charged systems, for obvious reasons.


On Thu, Apr 25, 2013 at 4:00 PM, ABEL Stephane 175950
stephane.a...@cea.frwrote:

 And ? sorry but i do not understand...

 Stephane

 --

 Message: 2
 Date: Thu, 25 Apr 2013 15:39:12 +0200
 From: Dr. Vitaly Chaban vvcha...@gmail.com
 Subject: Re: [gmx-users] Martini with PME, temp two low
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID:
 CAPXdD+bDiuQWG_3eWZ_0yb=
 aynlaaf08vt46usel4wk_bjg...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 Hmmm

 Aren't the keywords here charged system + PME?


 Dr. Vitaly Chaban



 On Thu, Apr 25, 2013 at 1:34 PM, XAvier Periole x.peri...@rug.nl wrote:

 
  Did you visualise the system? T in function of time? Epot in function of
  time?
 
  As a side note (not relevant for PME) the mix of nstlist = 10 and the
  rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and
  rlist=1.4 if nstlist =10.
 
  On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 stephane.a...@cea.fr
  wrote:
 
   Hello all,
  
   I am trying to test the martini force field with PME for a charged
  system that contains na+, water, surfactant, octane molecules at 298K and
  P=0.1MPa. My system works well, if i use the standard shift parameters
  (correct temp, and pressure). But for for the simulation with PME , the
  temp of the system decrease to  290 K. Below my *.mdp parameters for a
 NPT
  equil at 298K
  
  
   integrator   = md
   dt   = 0.020
   nsteps   = 1 ; 200ps
   nstcomm  = 10
   comm-grps=
   ;refcoord_scaling = com
  
   nstxout  = 0
   nstvout  = 0
   nstfout  = 0
   nstlog   = 1000
   nstenergy= 100
   ;nstxtcout= 1000
   xtc_precision= 100
   ;xtc-grps =
   energygrps   = AOT W ION OCT
  
   nstlist  = 10
   ns_type  = grid
   pbc  = xyz
   rlist= 1.
  
   ; PME parameters
   coulombtype  = PME
   rcoulomb = 1.2
   rvdw = 1.2
   fourierspacing   = 0.12
   fourier_nx   = 0
   fourier_ny   = 0
   fourier_nz   = 0
   pme_order= 4
  
   tcoupl   = v-rescale
   tc-grps  = AOT_W_ION OCT
   tau_t= 1.0 1.0
   ref_t= 298 298
   Pcoupl   = berendsen
   Pcoupltype   = isotropic
   tau_p= 1.0
   compressibility  = 4.5e-5
   ref_p= 1.0
  
   ;gen_vel  = no
   ;gen_temp = 0
   ;gen_seed = 473529
  
  
   ; MARTINI and CONSTRAINTS
   ; for ring systems and stiff bonds constraints are defined
   ; which are best handled using Lincs.
  
   constraints  = none
   constraint_algorithm = Lincs
   unconstrained_start  = no
   lincs_order  = 4
   lincs_warnangle  = 3
  
  
   Results obtained with W/ PME
  
 Statistics over 10001 steps using 1001 frames
  
 Energies (kJ/mol)
 Bond   G96AngleLJ (SR)   Coulomb (SR)   Coul.
  recip.
  1.63789e+041.25195e+03   -4.02093e+05   -8.22079e+03
  -4.86843e+04
PotentialKinetic En.   Total EnergyTemperature Pressure
  (bar)
 -4.41367e+057.81801e+04   -3.63187e+052.90373e+02
  -1.76470e+01
  T-AOT_W_ION  T-OCT
  2.90629e+022.90357e+02
  
   Results W:o PME
  
 Energies (kJ/mol)
 Bond   G96AngleLJ (SR)   Coulomb (SR)
   Potential
  1.60482e+041.24820e+03   -3.34608e+05   -7.33665e+02
  -3.18046e+05
  Kinetic En.   Total EnergyTemperature Pressure (bar)
  8.02685e+04   -2.3e+052.98129e+02   -3.07123e+01
  
Box-X  Box-Y  Box-Z
  1.52926e+011.52926e+011.52926e+01
  
  
  T-AOT_W_ION  T-OCT
  2.98141e+022.98129e+02
  
  
   Did I miss something ?
  
  
   Note that for the moment i do not use the polarizable water model.
  
   Thanks for your help
  
   Stephane
  
  
  

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[gmx-users] g_rmsf Analysis.

2013-04-25 Thread Vivek Modi

Hello,

I am using g_rmsf for analysis of a protein simulation. I want to calculate
the fluctuations with respect to a reference structure (using -od option).
But I am encountering a problem. Please correct me if I am wrong at some
place. The following two methods are giving me different results. I have
defined the residues forming helices as a separate group in the index file
(to exclude loops).

1. g_rmsf  -f abc.xtc -s abc.tpr -od rmsdev.xvg -n index
-- I choose  Protein_CA from the index file (full protein).

2. g_rmsf  -f abc.xtc -s abc.tpr -od rmsdev.xvg -n index
-- I choose helix_residues_CA from the index file (excluding loops).


For the same helical regions of the protein I am getting different results
from these two methods. The first one shows high fluctuations as compared
to the second. My guess is that it can be due to different fitting by the
choice of different atoms. But I suspect that the difference between the
two is quite big than to be caused by different fitting.

I also repeated the same analysis by dividing the trajectory into two parts
and comparing the fluctuations with each other and the for the complete
trajectory.
The output in this case from the first method was consistent. Same regions
were showing similar fluctuations. But for the second method the chunked
parts of the trajectory displayed very small movement in certain regions
where the complete trajectory analysis exhibited high fluctuations. How can
this be inconsistent for the same fitting.

Let me know if I am doing a mistake.


Thanks.

Vivek Modi

Graduate Student,
IITK.
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[gmx-users] Re: Martini with PME, temp two low

@ Vitaly
of course. I know that. My system is neutral  but with charged particles (AOT 
and Na+).  

@Xavier 
I will try your suggestion and equilibrate my system for a longer period

Thanks again

Stephane



--

Message: 1
Date: Thu, 25 Apr 2013 15:52:09 +0200
From: XAvier Periole x.peri...@rug.nl
Subject: Re: [gmx-users] Martini with PME, temp two low
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 0a7b7d0a-b419-4d3d-826b-e6d61de6d...@rug.nl
Content-Type: text/plain; charset=windows-1252


Well ? 400 ps is rather small and you can expect deviations from so short 
simulations if you start from an non-equilibrated system. I am not sure what 
the void is but this indicates that your system might not be equilibrated ?

You can try to decrease the time step and nstlist to see if you the drop of 
temperature is due a flow of energy.

On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote:

 Hello Xavier,

 Thank you for your response.

 nstlist = 10 and the rlist = 1.0
 My mistake, i did not changes these values when i switched to PME,

 I have rerun the simulations for 400 ps in NPT with these changes and plotted 
 Epot and Temp vs Time The Epot and Temp values are not stables. The average 
 Temp of the system  is better than previously but fluctuate around (294 K) 
 instead of 298 K . Note i use gmx4.5.5 to do my calculations.

 I have also visualized my  system at the end of the NPT run, the  na+, water, 
 surfactant, octane molecules  form a slab with void

 What's wrong ?

 Stephane



 --

 Message: 5
 Date: Thu, 25 Apr 2013 13:34:21 +0200
 From: XAvier Periole x.peri...@rug.nl
 Subject: Re: [gmx-users] Martini with PME, temp two low
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID: 4632c83b-cd6f-4c92-b887-a1c39dff4...@rug.nl
 Content-Type: text/plain; charset=us-ascii


 Did you visualise the system? T in function of time? Epot in function of time?

 As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist = 
 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 
 if nstlist =10.

 On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 stephane.a...@cea.fr 
 wrote:

 Hello all,

 I am trying to test the martini force field with PME for a charged system 
 that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. 
 My system works well, if i use the standard shift parameters (correct temp, 
 and pressure). But for for the simulation with PME , the temp of the system 
 decrease to  290 K. Below my *.mdp parameters for a NPT equil at 298K


 integrator   = md
 dt   = 0.020
 nsteps   = 1 ; 200ps
 nstcomm  = 10
 comm-grps=
 ;refcoord_scaling = com

 nstxout  = 0
 nstvout  = 0
 nstfout  = 0
 nstlog   = 1000
 nstenergy= 100
 ;nstxtcout= 1000
 xtc_precision= 100
 ;xtc-grps =
 energygrps   = AOT W ION OCT

 nstlist  = 10
 ns_type  = grid
 pbc  = xyz
 rlist= 1.

 ; PME parameters
 coulombtype  = PME
 rcoulomb = 1.2
 rvdw = 1.2
 fourierspacing   = 0.12
 fourier_nx   = 0
 fourier_ny   = 0
 fourier_nz   = 0
 pme_order= 4

 tcoupl   = v-rescale
 tc-grps  = AOT_W_ION OCT
 tau_t= 1.0 1.0
 ref_t= 298 298
 Pcoupl   = berendsen
 Pcoupltype   = isotropic
 tau_p= 1.0
 compressibility  = 4.5e-5
 ref_p= 1.0

 ;gen_vel  = no
 ;gen_temp = 0
 ;gen_seed = 473529


 ; MARTINI and CONSTRAINTS
 ; for ring systems and stiff bonds constraints are defined
 ; which are best handled using Lincs.

 constraints  = none
 constraint_algorithm = Lincs
 unconstrained_start  = no
 lincs_order  = 4
 lincs_warnangle  = 3


 Results obtained with W/ PME

  Statistics over 10001 steps using 1001 frames

  Energies (kJ/mol)
  Bond   G96AngleLJ (SR)   Coulomb (SR)   Coul. recip.
   1.63789e+041.25195e+03   -4.02093e+05   -8.22079e+03   -4.86843e+04
 PotentialKinetic En.   Total EnergyTemperature Pressure (bar)
  -4.41367e+057.81801e+04   -3.63187e+052.90373e+02   -1.76470e+01
   T-AOT_W_ION  T-OCT
   2.90629e+022.90357e+02

 Results W:o PME

  Energies (kJ/mol)
  Bond   G96AngleLJ (SR)   Coulomb (SR)  Potential
   1.60482e+041.24820e+03   -3.34608e+05   -7.33665e+02   -3.18046e+05
   Kinetic En.   Total EnergyTemperature

Re: [gmx-users] Martini with PME, temp two low




On 4/25/13 10:05 AM, Dr. Vitaly Chaban wrote:

PME should NOT be used with charged systems, for obvious reasons.




FYI Gromacs provides a neutralizing background charge.

http://comments.gmane.org/gmane.science.biology.gromacs.user/639

There may, of course, be issues with the physical reality of such a setup, but 
this is a common question.


-Justin


On Thu, Apr 25, 2013 at 4:00 PM, ABEL Stephane 175950
stephane.a...@cea.frwrote:


And ? sorry but i do not understand...

Stephane

--

Message: 2
Date: Thu, 25 Apr 2013 15:39:12 +0200
From: Dr. Vitaly Chaban vvcha...@gmail.com
Subject: Re: [gmx-users] Martini with PME, temp two low
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
 CAPXdD+bDiuQWG_3eWZ_0yb=
aynlaaf08vt46usel4wk_bjg...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1

Hmmm

Aren't the keywords here charged system + PME?


Dr. Vitaly Chaban



On Thu, Apr 25, 2013 at 1:34 PM, XAvier Periole x.peri...@rug.nl wrote:



Did you visualise the system? T in function of time? Epot in function of
time?

As a side note (not relevant for PME) the mix of nstlist = 10 and the
rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and
rlist=1.4 if nstlist =10.

On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 stephane.a...@cea.fr
wrote:


Hello all,

I am trying to test the martini force field with PME for a charged

system that contains na+, water, surfactant, octane molecules at 298K and
P=0.1MPa. My system works well, if i use the standard shift parameters
(correct temp, and pressure). But for for the simulation with PME , the
temp of the system decrease to  290 K. Below my *.mdp parameters for a

NPT

equil at 298K



integrator   = md
dt   = 0.020
nsteps   = 1 ; 200ps
nstcomm  = 10
comm-grps=
;refcoord_scaling = com

nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 1000
nstenergy= 100
;nstxtcout= 1000
xtc_precision= 100
;xtc-grps =
energygrps   = AOT W ION OCT

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.

; PME parameters
coulombtype  = PME
rcoulomb = 1.2
rvdw = 1.2
fourierspacing   = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order= 4

tcoupl   = v-rescale
tc-grps  = AOT_W_ION OCT
tau_t= 1.0 1.0
ref_t= 298 298
Pcoupl   = berendsen
Pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

;gen_vel  = no
;gen_temp = 0
;gen_seed = 473529


; MARTINI and CONSTRAINTS
; for ring systems and stiff bonds constraints are defined
; which are best handled using Lincs.

constraints  = none
constraint_algorithm = Lincs
unconstrained_start  = no
lincs_order  = 4
lincs_warnangle  = 3


Results obtained with W/ PME

   Statistics over 10001 steps using 1001 frames

   Energies (kJ/mol)
   Bond   G96AngleLJ (SR)   Coulomb (SR)   Coul.

recip.

1.63789e+041.25195e+03   -4.02093e+05   -8.22079e+03

-4.86843e+04

  PotentialKinetic En.   Total EnergyTemperature Pressure

(bar)

   -4.41367e+057.81801e+04   -3.63187e+052.90373e+02

-1.76470e+01

T-AOT_W_ION  T-OCT
2.90629e+022.90357e+02

Results W:o PME

   Energies (kJ/mol)
   Bond   G96AngleLJ (SR)   Coulomb (SR)

  Potential

1.60482e+041.24820e+03   -3.34608e+05   -7.33665e+02

-3.18046e+05

Kinetic En.   Total EnergyTemperature Pressure (bar)
8.02685e+04   -2.3e+052.98129e+02   -3.07123e+01

  Box-X  Box-Y  Box-Z
1.52926e+011.52926e+011.52926e+01


T-AOT_W_ION  T-OCT
2.98141e+022.98129e+02


Did I miss something ?


Note that for the moment i do not use the polarizable water model.

Thanks for your help

Stephane





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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

Re: [gmx-users] Doubt about the Gromacs versions




On 4/25/13 9:48 AM, Richard Broadbent wrote:

The 4.6.1 release is a more advanced version of gromacs with the latest kernels
and features (GPU support, verlet cut-offs etc.).

4.5.7 is a maintenance release for those of us who for whatever reason wish to
keep using the older 4.5.x series release. It mainly adds fixes made to the
4.6.x series to the 4.5.x version of the code. I use it as most of my
calculations were conducted in 4.5.5 so this version allows me to use exactly
the same setup as I was using before.

If you are starting a new project I would suggest that the 4.6.x series is what
you should use as it is substantially faster (for a system I'm running that
contains no water on an Intel sandy-bridge system it is more than 50% faster).
This series will also probably receive more attention in terms of bug fixes and
new releases (though I'm not a developer so I could be wrong about that).



Quite right.  4.5.7 is expected to be the last version in the 4.5.x series, and 
I suspect that will be true unless we discover some catastrophic bug that needs 
to be patched in older versions.  4.6.x (and the eventual transition to 5.0) 
will receive the greatest amount of attention from here on out.


-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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Re: [gmx-users] How to fix interfacial tension in NPT




On 4/25/13 9:10 AM, Souilem Safa wrote:

Dear Justin,
Please I want to ask you for the calculation of interfacial tension from
the formula : 1/2 (Pz - (px+py)/2))*Lz
Should I calculate the interfacial tension in every step and take the
average interfacial tension for all the steps or should I take the average
of the presssure tensors from all the steps and calculate the interfacial
tension which will be only one value? Because it gives different values.


Beyond my area of expertise.  Maybe someone who does this kind of work can 
answer this.


-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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Re: [gmx-users] g_rmsf Analysis.




On 4/25/13 10:12 AM, Vivek Modi wrote:

Hello,

I am using g_rmsf for analysis of a protein simulation. I want to calculate
the fluctuations with respect to a reference structure (using -od option).
But I am encountering a problem. Please correct me if I am wrong at some
place. The following two methods are giving me different results. I have
defined the residues forming helices as a separate group in the index file
(to exclude loops).

1. g_rmsf  -f abc.xtc -s abc.tpr -od rmsdev.xvg -n index
-- I choose  Protein_CA from the index file (full protein).

2. g_rmsf  -f abc.xtc -s abc.tpr -od rmsdev.xvg -n index
-- I choose helix_residues_CA from the index file (excluding loops).


For the same helical regions of the protein I am getting different results
from these two methods. The first one shows high fluctuations as compared
to the second. My guess is that it can be due to different fitting by the
choice of different atoms. But I suspect that the difference between the
two is quite big than to be caused by different fitting.



I would counter that differences in fitting can quite easily explain the 
difference you are seeing.  Without the actual numbers, it's hard to say exactly.



I also repeated the same analysis by dividing the trajectory into two parts
and comparing the fluctuations with each other and the for the complete
trajectory.
The output in this case from the first method was consistent. Same regions
were showing similar fluctuations. But for the second method the chunked
parts of the trajectory displayed very small movement in certain regions
where the complete trajectory analysis exhibited high fluctuations. How can
this be inconsistent for the same fitting.



Simply splitting the trajectory in half is not necessarily informative, 
especially if the structure is sampling different states, is not equilibrated in 
the beginning, etc.


-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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[gmx-users] How to use multiple nodes, each with 2 CPUs and 3 GPUs

2013-04-25 Thread Christopher Neale

Thank you Berk,

I am still getting an error when I try with MPI compiled gromacs 4.6.1 and -np 
set as you suggested.

I ran like this:
mpirun -np 6 /nics/b/home/cneale/exe/gromacs-4.6.1_cuda/exec2/bin/mdrun_mpi 
-notunepme -deffnm md3 -dlb yes -npme -1 -cpt 60 -maxh 0.1 -cpi md3.cpt -nsteps 
50 -pin on

Here is the .log file output:
Log file opened on Thu Apr 25 10:24:55 2013
Host: kfs064  pid: 38106  nodeid: 0  nnodes:  6
Gromacs version:VERSION 4.6.1
Precision:  single
Memory model:   64 bit
MPI library:MPI
OpenMP support: enabled
GPU support:enabled
invsqrt routine:gmx_software_invsqrt(x)
CPU acceleration:   AVX_256
FFT library:fftw-3.3.3-sse2
Large file support: enabled
RDTSCP usage:   enabled
Built on:   Tue Apr 23 12:43:12 EDT 2013
Built by:   cne...@kfslogin2.nics.utk.edu [CMAKE]
Build OS/arch:  Linux 2.6.32-220.4.1.el6.x86_64 x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
Build CPU family:   6   Model: 45   Stepping: 7
Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr 
nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 
sse4.2 ssse3 tdt x2apic
C compiler: /opt/intel/composer_xe_2011_sp1.11.339/bin/intel64/icc 
Intel icc (ICC) 12.1.5 20120612
C compiler flags:   -mavx   -std=gnu99 -Wall   -ip -funroll-all-loops  -O3 
-DNDEBUG
C++ compiler:   /opt/intel/composer_xe_2011_sp1.11.339/bin/intel64/icpc 
Intel icpc (ICC) 12.1.5 20120612
C++ compiler flags: -mavx   -Wall   -ip -funroll-all-loops  -O3 -DNDEBUG
CUDA compiler:  nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 
2005-2012 NVIDIA Corporation;Built on Thu_Apr__5_00:24:31_PDT_2012;Cuda 
compilation tools, release 4.2, V0.2.1221
CUDA driver:5.0
CUDA runtime:   4.20


 :-)  G  R  O  M  A  C  S  (-:

   Groningen Machine for Chemical Simulation

:-)  VERSION 4.6.1  (-:

Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, 
   Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,  
 Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, 
Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, 
   Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, 
Michael Shirts, Alfons Sijbers, Peter Tieleman,

   Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2012,2013, The GROMACS development team at
Uppsala University  The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
   modify it under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
 of the License, or (at your option) any later version.

:-)  /nics/b/home/cneale/exe/gromacs-4.6.1_cuda/exec2/bin/mdrun_mpi  (-:


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
  --- Thank You ---  


For optimal performance with a GPU nstlist (now 10) should be larger.
The optimum depends on your CPU and GPU resources.
You might want to try several nstlist values.
Can not increase nstlist for GPU run because verlet-buffer-drift is not set or 
used
Input Parameters:
   integrator   = sd
   nsteps   = 500
   init-step= 0
   cutoff-scheme= Verlet
   ns_type  = Grid
   nstlist  = 10
   ndelta   = 2
   nstcomm  = 100
   comm-mode= Linear
   nstlog   = 0
   nstxout  = 500
   nstvout  = 500
   nstfout  = 500
   nstcalcenergy= 100

Re: [gmx-users] How to fix interfacial tension in NPT

2013-04-25 Thread Souilem Safa

Thank you for your reply :) I will look further

On 25 April 2013 23:18, Justin Lemkul jalem...@vt.edu wrote:

On 4/25/13 9:10 AM, Souilem Safa wrote:

Dear Justin,
Please I want to ask you for the calculation of interfacial tension from
the formula : 1/2 (Pz - (px+py)/2))*Lz
Should I calculate the interfacial tension in every step and take the
average interfacial tension for all the steps or should I take the average
of the presssure tensors from all the steps and calculate the interfacial
tension which will be only one value? Because it gives different values.

Beyond my area of expertise. Maybe someone who does this kind of work can
answer this.

-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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==**==
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[gmx-users] interfacial-tension-interface simulation

2013-04-25 Thread Souilem Safa

Dear Gromacs users,

I'm simulating a water-oil interface. From litterature interfacial tension
is determined from pressure tensors as follows:1/2 (Pz - (px+py)/2))*Lz
Where Pz, Px and Py are the pressure tensors in the different axis.
I did a NPT simulation step and I want to check my interfacial tension
value.
Should I calculate the interfacial tension in every step and take the
average interfacial tension for all the steps or should I take the average
of the presssure tensors from all the steps and calculate the interfacial
tension which will be only one value? Because it gives different values.

Can any one help me in that? thanks
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Re: [gmx-users] How to use multiple nodes, each with 2 CPUs and 3 GPUs

2013-04-25 Thread Szilárd Páll

Hi,

You should really check out the documentation on how to use mdrun 4.6:
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Running_simulations

Brief summary: when running on GPUs every domain is assigned to a set
of CPU cores and a GPU, hence you need to start as many PP MPI ranks
per node as the number of GPUs (or pass a PP-GPU mapping manually).


Now, there are some slight complications with the inconvenient
hardware setup of the machines you are using. When the number of cores
is not divisible by the number of GPUs, you'll end up wasting cores.
In your case only 3*5=15 cores per compute node will be used. What
will make things even worse, unless you use -pin on (which is the
default behavior *only* if you use all cores in a node), is that mdrun
will not lock threads to cores and will let them be moved around by
the OS which can cause severe performance degradation .

However, you can actually work around these issues and get good
performance by using separate PME ranks. You can just try using 3 PP +
1 PME per compute node with four OpenMP threads each, i.e:
mpirun -np 4*Nnodes mpirun_mpi -npme 1 -ntomp 4
If you are lucky with the PP/PME load, this should work well and even
if you get some PP-PME imbalance, this should hurt performance way
less than the inconvenient 3x5 threads setup.

Cheers,
--
Szilárd


On Wed, Apr 24, 2013 at 7:08 PM, Christopher Neale
chris.ne...@mail.utoronto.ca wrote:
 Dear Users:

 I am having trouble getting any speedup by using more than one node,
 where each node has 2 8-core cpus and 3 GPUs. I am using gromacs 4.6.1.

 I saw this post, indicating that the .log file output about number of gpus 
 used might not be accurate:
 http://lists.gromacs.org/pipermail/gmx-users/2013-March/079802.html

 Still, I'm getting 21.2 ns/day on 1 node, 21.2 ns/day on 2 nodes, and 20.5 
 ns/day on 3 nodes.
 Somehow I think I have not configures the mpirun -np and mdrun -ntomp 
 correctly
 (although I have tried numerous combinations).

 On 1 node, I can just run mdrun without mpirun like this:
 http://lists.gromacs.org/pipermail/gmx-users/2013-March/079802.html

 For that run, the top of the .log file is:
 Log file opened on Wed Apr 24 11:36:53 2013
 Host: kfs179  pid: 59561  nodeid: 0  nnodes:  1
 Gromacs version:VERSION 4.6.1
 Precision:  single
 Memory model:   64 bit
 MPI library:thread_mpi
 OpenMP support: enabled
 GPU support:enabled
 invsqrt routine:gmx_software_invsqrt(x)
 CPU acceleration:   AVX_256
 FFT library:fftw-3.3.3-sse2
 Large file support: enabled
 RDTSCP usage:   enabled
 Built on:   Tue Apr 23 12:59:48 EDT 2013
 Built by:   cne...@kfslogin2.nics.utk.edu [CMAKE]
 Build OS/arch:  Linux 2.6.32-220.4.1.el6.x86_64 x86_64
 Build CPU vendor:   GenuineIntel
 Build CPU brand:Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
 Build CPU family:   6   Model: 45   Stepping: 7
 Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr 
 nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 
 sse4.2 ssse3 tdt x2apic
 C compiler: /opt/intel/composer_xe_2011_sp1.11.339/bin/intel64/icc 
 Intel icc (ICC) 12.1.5 20120612
 C compiler flags:   -mavx   -std=gnu99 -Wall   -ip -funroll-all-loops  -O3 
 -DNDEBUG
 C++ compiler:   /opt/intel/composer_xe_2011_sp1.11.339/bin/intel64/icpc 
 Intel icpc (ICC) 12.1.5 20120612
 C++ compiler flags: -mavx   -Wall   -ip -funroll-all-loops  -O3 -DNDEBUG
 CUDA compiler:  nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 
 2005-2012 NVIDIA Corporation;Built on Thu_Apr__5_00:24:31_PDT_2012;Cuda 
 compilation tools, release 4.2, V0.2.1221
 CUDA driver:5.0
 CUDA runtime:   4.20
 ...
 snip
 ...
 Initializing Domain Decomposition on 3 nodes
 Dynamic load balancing: yes
 Will sort the charge groups at every domain (re)decomposition
 Initial maximum inter charge-group distances:
 two-body bonded interactions: 0.431 nm, LJ-14, atoms 101 108
   multi-body bonded interactions: 0.431 nm, Proper Dih., atoms 101 108
 Minimum cell size due to bonded interactions: 0.475 nm
 Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.175 nm
 Estimated maximum distance required for P-LINCS: 1.175 nm
 This distance will limit the DD cell size, you can override this with -rcon
 Using 0 separate PME nodes, per user request
 Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
 Optimizing the DD grid for 3 cells with a minimum initial size of 1.469 nm
 The maximum allowed number of cells is: X 5 Y 5 Z 6
 Domain decomposition grid 3 x 1 x 1, separate PME nodes 0
 PME domain decomposition: 3 x 1 x 1
 Domain decomposition nodeid 0, coordinates 0 0 0

 Using 3 MPI threads
 Using 5 OpenMP threads per tMPI thread

 Detecting CPU-specific acceleration.
 Present hardware specification:
 Vendor: GenuineIntel
 Brand:  Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
 Family:  6  Model: 45  Stepping:  7
 Features: aes apic avx

[gmx-users] Re: How to use multiple nodes, each with 2 CPUs and 3 GPUs

2013-04-25 Thread Christopher Neale

Dear Szilárd:

Thank you for your assistance. I understand the importance of reading the 
documentation and I read it about 5 times before I posted to this list. In 
fact, it's kind of buried in my initial post, but I did run MPI gromacs with 
mpirun -np 3 the first time and it didn't work.

I have finally realized that my problems are based on a PBS variable. 
Previously, I was using 
#PBS -l walltime=00:10:00,nodes=2:ppn=12:gpus=3:shared
I chose that because it was what was recommended on the webpage of the new 
cluster that I am using.

However, I can only get things to work when I use ppn=3 instead:
#PBS -l walltime=00:10:00,nodes=2:ppn=3:gpus=3:shared

That surprises me, because I thought that the mpirun -np option should take 
care of things, but in any event this has solved my general problem, which was 
that I could not get it running across multiple nodes at all. Now that I have 
this, I will take a look at your great suggestions about ranks, which I hadn't 
had the chance to explore because my #PBS ppn setting was stopping these runs 
from ever getting going.

Thank you again for your help.

Chris.

-- original message --

Hi,

You should really check out the documentation on how to use mdrun 4.6:
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Running_simulations

Brief summary: when running on GPUs every domain is assigned to a set
of CPU cores and a GPU, hence you need to start as many PP MPI ranks
per node as the number of GPUs (or pass a PP-GPU mapping manually).


Now, there are some slight complications with the inconvenient
hardware setup of the machines you are using. When the number of cores
is not divisible by the number of GPUs, you'll end up wasting cores.
In your case only 3*5=15 cores per compute node will be used. What
will make things even worse, unless you use -pin on (which is the
default behavior *only* if you use all cores in a node), is that mdrun
will not lock threads to cores and will let them be moved around by
the OS which can cause severe performance degradation .

However, you can actually work around these issues and get good
performance by using separate PME ranks. You can just try using 3 PP +
1 PME per compute node with four OpenMP threads each, i.e:
mpirun -np 4*Nnodes mpirun_mpi -npme 1 -ntomp 4
If you are lucky with the PP/PME load, this should work well and even
if you get some PP-PME imbalance, this should hurt performance way
less than the inconvenient 3x5 threads setup.

Cheers,
-- 
Szilárd

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[gmx-users] free energy of system

2013-04-25 Thread sarah k

Dear all,

I'm interested in calculating the Gibbs free energy of some systems. I
have several questions in this regard:

1- The g_energy command gives some values in kJ/mol for total energy
and enthalpy. Does the reported total energy include entropy effects?
(The calculated total energy and enthalpy were not equal for the
systems I had simulated.) Is the unit really kJ/mol?
2- Is it possible to perform md simulation as usual (like in the
drug-enzyme tutorial) and run the g_bar command to get the dG results?
3- How can I get the md_$LAMBDA.mdp file? Or which lines should be
added to the common md.mdp files?

Best regards,
Sarah Keshavarz
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[gmx-users] Re: Martini with PME, temp two low (ABEL Stephane 175950)

Xavier 

I have followed your suggestion and did a longer NPT equilibration with smaller 
dt and ntlist values and It works. The Energy and Temp  reach to stables values 
as i want. 

 thank you again  for your help

Stephane

--

Message: 2
Date: Thu, 25 Apr 2013 14:17:00 +
From: ABEL Stephane 175950 stephane.a...@cea.fr
Subject: [gmx-users] Re: Martini with PME, temp two low
To: gmx-users@gromacs.org gmx-users@gromacs.org
Message-ID:
3e39b768bb199548ab18f7289e7534af1a818...@exdag0-b0.intra.cea.fr
Content-Type: text/plain; charset=us-ascii

@ Vitaly
of course. I know that. My system is neutral  but with charged particles (AOT 
and Na+).

@Xavier
I will try your suggestion and equilibrate my system for a longer period

Thanks again

Stephane



--

Message: 1
Date: Thu, 25 Apr 2013 15:52:09 +0200
From: XAvier Periole x.peri...@rug.nl
Subject: Re: [gmx-users] Martini with PME, temp two low
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 0a7b7d0a-b419-4d3d-826b-e6d61de6d...@rug.nl
Content-Type: text/plain; charset=windows-1252


Well ? 400 ps is rather small and you can expect deviations from so short 
simulations if you start from an non-equilibrated system. I am not sure what 
the void is but this indicates that your system might not be equilibrated ?

You can try to decrease the time step and nstlist to see if you the drop of 
temperature is due a flow of energy.

On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote:

 Hello Xavier,

 Thank you for your response.

 nstlist = 10 and the rlist = 1.0
 My mistake, i did not changes these values when i switched to PME,

 I have rerun the simulations for 400 ps in NPT with these changes and plotted 
 Epot and Temp vs Time The Epot and Temp values are not stables. The average 
 Temp of the system  is better than previously but fluctuate around (294 K) 
 instead of 298 K . Note i use gmx4.5.5 to do my calculations.

 I have also visualized my  system at the end of the NPT run, the  na+, water, 
 surfactant, octane molecules  form a slab with void

 What's wrong ?

 Stephane

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Re: [gmx-users] free energy of system




On 4/25/13 12:02 PM, sarah k wrote:

Dear all,

I'm interested in calculating the Gibbs free energy of some systems. I
have several questions in this regard:

1- The g_energy command gives some values in kJ/mol for total energy
and enthalpy. Does the reported total energy include entropy effects?


Not likely.


(The calculated total energy and enthalpy were not equal for the
systems I had simulated.) Is the unit really kJ/mol?


Total energy and enthalpy should not necessarily be equal.  Total energy is just 
the sum of potential and kinetic energy.  The unit of kJ/mol is actually kJ per 
mole of equivalent systems.



2- Is it possible to perform md simulation as usual (like in the
drug-enzyme tutorial) and run the g_bar command to get the dG results?


That depends on your definition of as usual and what you expect as a result. 
You can decouple a ligand from a binding site, but that only gives you part of 
the information you need to calculate, for instance, the actual free energy of 
binding.



3- How can I get the md_$LAMBDA.mdp file? Or which lines should be
added to the common md.mdp files?



Given the nomenclature, I assume you are referring to files in my free energy 
tutorial, which are created by scripts.  All the answers to this question are in 
my tutorial.


-Justin

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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 gromacs in Cluster

This works well until you use a system that permits job suspension. Then
-maxh gets double-crossed... :-)

Mark
On Apr 25, 2013 3:41 PM, Richard Broadbent 
richard.broadben...@imperial.ac.uk wrote:

 I generally build a tpr for the whole simulation then submit one job using
 a command such as:

 mpirun -n ${NUM_PROCESSORS} mdrun -deffnm ${NAME} -maxh
 ${WALL_TIME_IN_HOURS}

 copy all the files back at the end of the script if necessary then:

 then resubmit it (sending out all the files again if necessary) this time
 using the command

 mpirun -n ${NUM_PROCESSORS} mdrun -deffnm ${NAME} -maxh
 ${WALL_TIME_IN_HOURS} -cpi

 you can then keep resubmitting with that line till the job is finished.

 In my case I have a maximum wall clock of 24hrs on some machines so this
 gets used a lot

 I also think that 1.6ns/day which is what you seem to be getting is very
 low performance and you might want to consider using more processors. Check
 the log file as the profiling information at the end will indicate whether
 this might be beneficial.

 Richard


 On 25/04/13 13:58, Francesco wrote:

 You can split the simulation in different part (for example 5 ns each),
 every time you'll finish one you will extend it adding more time.
 http://www.gromacs.org/**Documentation/How-tos/**Extending_Simulations?**
 highlight=extendhttp://www.gromacs.org/Documentation/How-tos/Extending_Simulations?highlight=extend

 My cluster uses a different script system than yours so I can't help
 with it, but basically you have to submit more than 1 job with different
 command to execute:

 1) first production
 mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8
 2) modify the tpr file
 tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
 3) next X ns
 mpirun -n 8 mdrun -s next.tpr -cpi previous.cpt
 4) modify the tpr file
 5) production md
 and so on

 with qsub you can submit a depending job (-hold_jid) that will run only
 when the previous step will finish, in your case there should be a
 similar way to do it.

 cheers

 Fra

 On Thu, 25 Apr 2013, at 12:28 PM, Sainitin Donakonda wrote:

 Hey all,

 I recently ran 20ns simulation of protein ligand complex on cluster i
 used
 following script to run simulation

 grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
 md_test.tpr

 mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8

 *I saved this as MD.sh And then submited to cluster using following
 script*

 #!/bin/bash
 #BSUB -J testgromacs # the job's name/array job
 #BSUB -W 120:00   # max. wall clock time in hh:mm
 #BSUB -n 8,8  # number of processors Min,Max
 #BSUB -o test/output_%J.log # output file
 #BSUB -e test/errors_%J.log # error file
 #BSUB -M 8192 #Memory limit in MB

 echo Started at `date`
 echo

 cd test

 echo Running gromacs test in `pwd`

 ./MD.sh

 echo Finished at `date`


 It gave result but when checked files .xtc and created RMSD plots in that
 x-axis of this plot i see only 8ns ...but in MD.MDP file i specified
 20ns..

 Cluster Output says that TERM_RUNLIMIT: job killed after reaching LSF
 run
 time limit.
 Exited with exit code 140. i gave maximum cluster time 120 hours..still
 it
 is not sufficient ..

 Can any body tell me  how do it split script i such  that i will get all
 20ns simulation


 Thanks in advance ,

 Sainitin
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[gmx-users] How to rescue trr trajectory when two or more corrupted frames exist

2013-04-25 Thread Ioannis Beis

Dear Gromacs users,

I have some corrupted frames in different trajectories. gmxcheck with .trr 
trajectories gives extraordinary positions or velocities and with .xtc 
trajectories gives rise to the magic number error. I am aware of the program 
gmx_rescue kindly offered to us by its developers. However, this program can 
only work with .xtc files. It is possible to rescue .trr files when there is a 
maximum of one corrupted frame by checking the size of healthy frames, chopping 
the parts of the trajectory before and after, using e.g. programs head and tail 
with the corresponding integer multiples of one healthy frame in bytes and 
stitching them together. However, when there is two or more corrupted frames in 
different locations, although it is not hard to spot the exact locations, it is 
no longer possible to remove the problematic frames size-wise (or at least it 
is less likely to succeed than winning the lottery) , since the size of each 
corrupted frame is non-standard. Is there any corresponding software to 
gmx_rescue that can be used with .trr files? Is there any other recent program 
or any other way of coping with the problem? I did not post any details of my 
systems or the specific error messages I get because I believe my question is 
clear.

Thank you in advance!

Best,
Yiannis
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Re: [gmx-users] RMSD from the average structure

2013-04-25 Thread Tsjerk Wassenaar

Hi Bipin Singh,

That indeed gives you the RMSD against the average. Do think about it a bit
more: do you want the average of the whole structure, or should you account
for a phase of relaxation?

Cheers,

Tsjerk


On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 4/24/13 3:06 AM, bipin singh wrote:

 Hi all,

 Please let me know whether this is the right way to calculate RMSD from
 the
 average structure from a simulation:

 g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg


 average.pdb: is the pdb file produced using -ox option of g_rmsf.


 You can calculate RMSD with respect to whatever structure you like, but
 the interpretation and justification for doing so are up to you.

 -Justin

 --
 ==**==

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

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Re: [gmx-users] issue in replica exchange

Thanks for the good report. There have been some known issues about the
timing of coupling stages with respect to various intervals between GROMACS
events for some algorithms. There are a lot of fixed problems in 4.5.7 that
are not specific to REMD, but I have a few lingering doubts about whether
we should be exchanging (scaled) coupling values along with the
coordinates. (Unlike most REMD implementations, GROMACS swaps the
coordinates, not the ensemble data.) If you can reproduce those kinds of
symptoms in 4.5.7 (whether or not they then crash) then there looks like
there may be a problem with the REMD implementation that is perhaps evident
only with the kind of large time step Martini takes?

Mark


On Thu, Apr 25, 2013 at 1:28 PM, XAvier Periole x.peri...@rug.nl wrote:


 Hi,

 I have been recently using the REMD code in gmx-407 and gmx-453 and got a
 few systems crashing for unclear reasons so far. The main tests I made are
 using gmx407 but it is all reproducible with gmx453. The crashing was also
 reproduced (not necessarily at the same time point) on several
 architectures.

 The system is made of a pair of proteins in a membrane patch and for which
 the relative orientation is controlled by non-native bond/angles/dihedrals
 to perform an umbrella sampling. I use the MARTINI force field but that
 might not be relevant here.

 The crashes occur following exchanges that do not seem to occur the
 correct way and preceded by pressure scaling warnings … indicative of a
 strong destabilisation of the system and eventual explosion. Some
 information seems to be exchanged inaccurately.

 Trying to nail down the problem I got stuck and may be some one can help.
 I placed a pdf file showing plots of bonded/nonbonded energies,
 temperatures, box size etc … around an exchange that does not lead to a
 crash (here: md.chem.rug.nl/~periole/remd-issue.pdf). I plotted stuff
 every step with the temperature colour coded as indicated in the first
 figure.

 From the figure it appears that the step right after the exchange there is
 a huge jump of Potential energy coming from the LJ(SR) part of it. Although
 there are some small discontinuities in the progression of the bond and
 angle energy around the exchange they seem to fine. The temperature and box
 size seem to respond to it a few step latter while the pressure seems to be
 affected right away but potentially as the Epot will affect the viral and
 thus the Pressure.

 The other potential clue is that the jumps reduce with the strength of the
 pressure coupling. A 1/2 ps tau_p (Berendsen) will lead to a crash while a
 5/10/20 ps won't. Inspection of the time evolution of the Epot, box …
 indicates that the magnitude of the jumps is reduced and the system ca
 handle the problem.

 One additional info since I first posted the problem (delayed by the file
 first attached but now given with a link) the problem is accentuated when
 the replicas differ in conformation. I am looking at the actual differences
 as you'll read this email.

 That is as far as I could go. Any suggestion is welcome.

 XAvier.
 MD-Group / Univ. of Groningen
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Re: [gmx-users] Fwd: Selecting the temperature distribution

Yes,  I got exchanges. By construction! :-)

Email me off-list if you would like a methods description (for what it is
worth).

Mark


On Thu, Apr 25, 2013 at 1:11 PM, massimo sandal deviceran...@gmail.comwrote:

 This hints at an interesting protocol/attempt, at least for a sort of
 newbie like me. Can you elaborate? Did they exchange?
 On 25 Apr 2013 13:06, Mark Abraham mark.j.abra...@gmail.com wrote:

  Likewise, I agreed with what Massimo said.
 
  As an example, I recently did a fairly large set of REMD simulations of a
  320-atom disordered peptide with rather more water and many fewer
 replicas
  than you propose. I did so because I expected low barriers and large
  maximum diameter (the latter from an implicit-solvent REMD). Even after
 the
  fact, I cannot demonstrate that my decisions were correct (and probably
  could not even if I could have produced clearly converged ensembles).
 
  Mark
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Re: [gmx-users] Fwd: amber03 force field

X-C-CN-X is not present in amber03 in the GROMACS distribution. You seem to
be using some modified version. Please ask the person who modified it :-)

Mark


On Wed, Apr 24, 2013 at 4:26 PM, Elisa Frezza elisa.fre...@gmail.comwrote:

 Dear All,

 I am starting to use amber03 force field, but I have found something very
 strange for proper angle dihedral.

 On the basis of definition of proper dihedral function in AMBER and GROMACS
 manual I aspect that the following conversion from amber to gromacs:

 k_n(GROMACS)=4.18/2 V_n (AMBER)

 where n= multiplicity.

 If I compare ffbonded.itp file in ffamber03 folder and the parameter
 reported in amber I find something very strange and I do not understand
 what it is right:

constant   angle
multiplicity
 AMBER:   X   CCNX8.00 180 2
 GROMACS   X   CCNX  16.736180 2
# kn= 4.18/2 V_n

constant   angle
multiplicity
 AMBER:   X   CNAX5.648 180
 2
 GROMACS   X   CNAX5.648 180 2
  # kn= 4.18/4 V_n

 the ratios between kn and Vn are different.
 Have someone some suggestions or explanation?

 Thanks in advance

 Elisa

 --
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 Phone: +39 049 827 5149
 Skype: elisa.frezza
 Emai: elisa.fre...@gmail.com
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 --
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 via Marzolo, 1
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Re: [gmx-users] Manual installation of new analysis tool

On Wed, Apr 24, 2013 at 8:14 AM, Venkat Reddy venkat...@gmail.com wrote:

 Dear all,
 I have got  an analysis tool for analyzing membrane density from Dr.Luca
 monticelli. I have followed the installation instructions as given.

 1) First thing is to load GROMACS
$ *source /usr/local/gromacs/bin/GMXRC*
 2) Enter the source directory of the program then make
$ cd g_mydensity
$ make
 According to the instructions, it should create an executable
 *g_mydensity*
 but I am getting the following errors

 *cc `pkg-config --libs libgmx`  g_mydensity.o matrix.o distances.o


Looks like his Makefile is relying on valid pkg-config registration. I've
no idea for what GROMACS versions under what conditions pkg-config actually
works, but I suggest you follow his instructions really precisely, and/or
contact him to resolve any doubtful points.

Mark


 dist_mode.o grid_mode.o   -o g_mydensity*
 *g_mydensity.o: In function `gmx_log2':*
 *g_mydensity.c:(.text+0xa8): undefined reference to `log'*
 *g_mydensity.o: In function `gmx_invsqrt':*
 *g_mydensity.c:(.text+0xf2): undefined reference to `gmx_invsqrt_exptab'*
 *g_mydensity.c:(.text+0x101): undefined reference to
 `gmx_invsqrt_fracttab'*
 *g_mydensity.o: In function `matrix_convert':*
 *g_mydensity.c:(.text+0x381): undefined reference to `cos'*
 *g_mydensity.c:(.text+0x3ad): undefined reference to `sin'*
 *g_mydensity.c:(.text+0x3da): undefined reference to `cos'*
 *g_mydensity.c:(.text+0x403): undefined reference to `cos'*
 *g_mydensity.c:(.text+0x416): undefined reference to `cos'*
 *g_mydensity.c:(.text+0x429): undefined reference to `cos'*
 *g_mydensity.c:(.text+0x447): undefined reference to `sin'*
 *g_mydensity.c:(.text+0x4ad): undefined reference to `sqrt'*
 *g_mydensity.o: In function `get_electrons':*
 *g_mydensity.c:(.text+0x527): undefined reference to `ffopen'*
 *g_mydensity.c:(.text+0x564): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0x5b6): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0x600): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0x62e): undefined reference to `save_calloc'*
 *g_mydensity.c:(.text+0x68d): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0x6eb): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0x74f): undefined reference to `ffclose'*
 *g_mydensity.o: In function `center_coords':*
 *g_mydensity.c:(.text+0x88f): undefined reference to `calc_box_center'*
 *g_mydensity.o: In function `calc_electron_density':*
 *g_mydensity.c:(.text+0x945): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0x973): undefined reference to `read_first_x'*
 *g_mydensity.c:(.text+0x9a0): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0xa38): undefined reference to `save_calloc'*
 *g_mydensity.c:(.text+0xa81): undefined reference to `save_calloc'*
 *g_mydensity.c:(.text+0xac1): undefined reference to `save_calloc'*
 *g_mydensity.c:(.text+0xaf6): undefined reference to `gmx_rmpbc_init'*
 *g_mydensity.c:(.text+0xb18): undefined reference to `set_pbc'*
 *g_mydensity.c:(.text+0xb38): undefined reference to `gmx_rmpbc'*
 *g_mydensity.c:(.text+0xe0b): undefined reference to `read_next_x'*
 *g_mydensity.c:(.text+0xe1e): undefined reference to `gmx_rmpbc_done'*
 *g_mydensity.c:(.text+0xe29): undefined reference to `close_trj'*
 *g_mydensity.c:(.text+0xecc): undefined reference to `save_free'*
 *g_mydensity.o: In function `calc_density':*
 *g_mydensity.c:(.text+0xf32): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0xf60): undefined reference to `read_first_x'*
 *g_mydensity.c:(.text+0xf8d): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0x101c): undefined reference to `save_calloc'*
 *g_mydensity.c:(.text+0x1065): undefined reference to `save_calloc'*
 *g_mydensity.c:(.text+0x10a5): undefined reference to `save_calloc'*
 *g_mydensity.c:(.text+0x10da): undefined reference to `gmx_rmpbc_init'*
 *g_mydensity.c:(.text+0x10fc): undefined reference to `set_pbc'*
 *g_mydensity.c:(.text+0x111c): undefined reference to `gmx_rmpbc'*
 *g_mydensity.c:(.text+0x143a): undefined reference to `read_next_x'*
 *g_mydensity.c:(.text+0x144d): undefined reference to `gmx_rmpbc_done'*
 *g_mydensity.c:(.text+0x146e): undefined reference to `close_trj'*
 *g_mydensity.c:(.text+0x1511): undefined reference to `save_free'*
 *g_mydensity.o: In function `plot_density':*
 *g_mydensity.c:(.text+0x159c): undefined reference to `xvgropen'*
 *g_mydensity.c:(.text+0x15bf): undefined reference to `xvgr_legend'*
 *g_mydensity.c:(.text+0x16ea): undefined reference to `ffclose'*
 *g_mydensity.o: In function `gmx_mydensity':*
 *g_mydensity.c:(.text+0x18bd): undefined reference to `CopyRight'*
 *g_mydensity.c:(.text+0x1923): undefined reference to `parse_common_args'*
 *g_mydensity.c:(.text+0x19a0): undefined reference to `ftp2fn'*
 *g_mydensity.c:(.text+0x19af): undefined reference to `read_top'*
 *g_mydensity.c:(.text+0x1a84): undefined reference to `save_calloc'*

Re: [gmx-users] issue in replica exchange


Thanks for the answer. I'll check gmx4.5.7 and report back. 

I am not sure what you mean by GROMACS swaps the coordinates not the ensemble 
data. The coupling to P and T and not exchanged with it? That would explain 
what I see, but let see what 4.5.7 has to say first. 

Tks. 

On Apr 25, 2013, at 22:40, Mark Abraham mark.j.abra...@gmail.com wrote:

 Thanks for the good report. There have been some known issues about the
 timing of coupling stages with respect to various intervals between GROMACS
 events for some algorithms. There are a lot of fixed problems in 4.5.7 that
 are not specific to REMD, but I have a few lingering doubts about whether
 we should be exchanging (scaled) coupling values along with the
 coordinates. (Unlike most REMD implementations, GROMACS swaps the
 coordinates, not the ensemble data.) If you can reproduce those kinds of
 symptoms in 4.5.7 (whether or not they then crash) then there looks like
 there may be a problem with the REMD implementation that is perhaps evident
 only with the kind of large time step Martini takes?
 
 Mark
 
 
 On Thu, Apr 25, 2013 at 1:28 PM, XAvier Periole x.peri...@rug.nl wrote:
 
 
 Hi,
 
 I have been recently using the REMD code in gmx-407 and gmx-453 and got a
 few systems crashing for unclear reasons so far. The main tests I made are
 using gmx407 but it is all reproducible with gmx453. The crashing was also
 reproduced (not necessarily at the same time point) on several
 architectures.
 
 The system is made of a pair of proteins in a membrane patch and for which
 the relative orientation is controlled by non-native bond/angles/dihedrals
 to perform an umbrella sampling. I use the MARTINI force field but that
 might not be relevant here.
 
 The crashes occur following exchanges that do not seem to occur the
 correct way and preceded by pressure scaling warnings … indicative of a
 strong destabilisation of the system and eventual explosion. Some
 information seems to be exchanged inaccurately.
 
 Trying to nail down the problem I got stuck and may be some one can help.
 I placed a pdf file showing plots of bonded/nonbonded energies,
 temperatures, box size etc … around an exchange that does not lead to a
 crash (here: md.chem.rug.nl/~periole/remd-issue.pdf). I plotted stuff
 every step with the temperature colour coded as indicated in the first
 figure.
 
 From the figure it appears that the step right after the exchange there is
 a huge jump of Potential energy coming from the LJ(SR) part of it. Although
 there are some small discontinuities in the progression of the bond and
 angle energy around the exchange they seem to fine. The temperature and box
 size seem to respond to it a few step latter while the pressure seems to be
 affected right away but potentially as the Epot will affect the viral and
 thus the Pressure.
 
 The other potential clue is that the jumps reduce with the strength of the
 pressure coupling. A 1/2 ps tau_p (Berendsen) will lead to a crash while a
 5/10/20 ps won't. Inspection of the time evolution of the Epot, box …
 indicates that the magnitude of the jumps is reduced and the system ca
 handle the problem.
 
 One additional info since I first posted the problem (delayed by the file
 first attached but now given with a link) the problem is accentuated when
 the replicas differ in conformation. I am looking at the actual differences
 as you'll read this email.
 
 That is as far as I could go. Any suggestion is welcome.
 
 XAvier.
 MD-Group / Univ. of Groningen
 The Netherlands--
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[gmx-users] Re: Manual installation of new analysis tool

2013-04-25 Thread Christoph Junghans

 Date: Thu, 25 Apr 2013 22:57:55 +0200
 From: Mark Abraham mark.j.abra...@gmail.com
 Subject: Re: [gmx-users] Manual installation of new analysis tool
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID:
 CAMNuMAT=tt7EJxdngFaVCK=4wko947kc_y7s_gsyrxg8nms...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 On Wed, Apr 24, 2013 at 8:14 AM, Venkat Reddy venkat...@gmail.com wrote:

 Dear all,
 I have got  an analysis tool for analyzing membrane density from Dr.Luca
 monticelli. I have followed the installation instructions as given.

 1) First thing is to load GROMACS
$ *source /usr/local/gromacs/bin/GMXRC*
 2) Enter the source directory of the program then make
$ cd g_mydensity
$ make
 According to the instructions, it should create an executable
 *g_mydensity*
 but I am getting the following errors

 *cc `pkg-config --libs libgmx`  g_mydensity.o matrix.o distances.o


 Looks like his Makefile is relying on valid pkg-config registration. I've
 no idea for what GROMACS versions under what conditions pkg-config actually
 works, but I suggest you follow his instructions really precisely, and/or
 contact him to resolve any doubtful points.
I added the pkg-config support with version 4.0.7 if I remember correctly.
Without knowing further details, two things come to my mind:
0.) [Trivial] Make sure that pkg-config is actually installed.
1.) Try if
$ pkg-config --libs libgmx
returns some useful output like -lgmx -lm. If not, you might need to
set PKG_CONFIG_PATH to ${GMXLDLIB}/pkgconfig, but normally GMXRC does
that for you automatically.
2.) Some functions in libgmx have been renamed/changed in the
development from 4.0 to 4.5 to 4.6, so you might actually need to
change the code, or use the same version as Dr.Luca Monticelli.

Cheers,

Christoph



 Mark


 dist_mode.o grid_mode.o   -o g_mydensity*
 *g_mydensity.o: In function `gmx_log2':*
 *g_mydensity.c:(.text+0xa8): undefined reference to `log'*
 *g_mydensity.o: In function `gmx_invsqrt':*
 *g_mydensity.c:(.text+0xf2): undefined reference to `gmx_invsqrt_exptab'*
 *g_mydensity.c:(.text+0x101): undefined reference to
 `gmx_invsqrt_fracttab'*
 *g_mydensity.o: In function `matrix_convert':*
 *g_mydensity.c:(.text+0x381): undefined reference to `cos'*
 *g_mydensity.c:(.text+0x3ad): undefined reference to `sin'*
 *g_mydensity.c:(.text+0x3da): undefined reference to `cos'*
 *g_mydensity.c:(.text+0x403): undefined reference to `cos'*
 *g_mydensity.c:(.text+0x416): undefined reference to `cos'*
 *g_mydensity.c:(.text+0x429): undefined reference to `cos'*
 *g_mydensity.c:(.text+0x447): undefined reference to `sin'*
 *g_mydensity.c:(.text+0x4ad): undefined reference to `sqrt'*
 *g_mydensity.o: In function `get_electrons':*
 *g_mydensity.c:(.text+0x527): undefined reference to `ffopen'*
 *g_mydensity.c:(.text+0x564): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0x5b6): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0x600): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0x62e): undefined reference to `save_calloc'*
 *g_mydensity.c:(.text+0x68d): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0x6eb): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0x74f): undefined reference to `ffclose'*
 *g_mydensity.o: In function `center_coords':*
 *g_mydensity.c:(.text+0x88f): undefined reference to `calc_box_center'*
 *g_mydensity.o: In function `calc_electron_density':*
 *g_mydensity.c:(.text+0x945): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0x973): undefined reference to `read_first_x'*
 *g_mydensity.c:(.text+0x9a0): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0xa38): undefined reference to `save_calloc'*
 *g_mydensity.c:(.text+0xa81): undefined reference to `save_calloc'*
 *g_mydensity.c:(.text+0xac1): undefined reference to `save_calloc'*
 *g_mydensity.c:(.text+0xaf6): undefined reference to `gmx_rmpbc_init'*
 *g_mydensity.c:(.text+0xb18): undefined reference to `set_pbc'*
 *g_mydensity.c:(.text+0xb38): undefined reference to `gmx_rmpbc'*
 *g_mydensity.c:(.text+0xe0b): undefined reference to `read_next_x'*
 *g_mydensity.c:(.text+0xe1e): undefined reference to `gmx_rmpbc_done'*
 *g_mydensity.c:(.text+0xe29): undefined reference to `close_trj'*
 *g_mydensity.c:(.text+0xecc): undefined reference to `save_free'*
 *g_mydensity.o: In function `calc_density':*
 *g_mydensity.c:(.text+0xf32): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0xf60): undefined reference to `read_first_x'*
 *g_mydensity.c:(.text+0xf8d): undefined reference to `gmx_fatal'*
 *g_mydensity.c:(.text+0x101c): undefined reference to `save_calloc'*
 *g_mydensity.c:(.text+0x1065): undefined reference to `save_calloc'*
 *g_mydensity.c:(.text+0x10a5): undefined reference to `save_calloc'*
 *g_mydensity.c:(.text+0x10da): undefined reference to `gmx_rmpbc_init'*
 *g_mydensity.c:(.text+0x10fc): undefined reference to `set_pbc'*
 *g_mydensity.c:(.text+0x111c): undefined

Re: [gmx-users] RMSD from the average structure

2013-04-25 Thread bipin singh

Thanks for your reply.
Actually I am interested to see how much structural deviation is occurring
in a protein during the simulation from its average position of atoms
rather than the initial position (crystal structure or starting structure).
The motivation of doing this analysis is the fact that in real solution
phase, a system may not be static and if we consider the time average
structure of a simulation to be the real representative of the structure in
solution phase rather than static crystal structure.







On Fri, Apr 26, 2013 at 2:06 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Hi Bipin Singh,

 That indeed gives you the RMSD against the average. Do think about it a bit
 more: do you want the average of the whole structure, or should you account
 for a phase of relaxation?

 Cheers,

 Tsjerk


 On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul jalem...@vt.edu wrote:

 
 
  On 4/24/13 3:06 AM, bipin singh wrote:
 
  Hi all,
 
  Please let me know whether this is the right way to calculate RMSD from
  the
  average structure from a simulation:
 
  g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg
 
 
  average.pdb: is the pdb file produced using -ox option of g_rmsf.
 
 
  You can calculate RMSD with respect to whatever structure you like, but
  the interpretation and justification for doing so are up to you.
 
  -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
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 
  ==**==
 
  --
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  http://lists.gromacs.org/**mailman/listinfo/gmx-users
 http://lists.gromacs.org/mailman/listinfo/gmx-users
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 http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting!
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 --
 Tsjerk A. Wassenaar, Ph.D.
 --
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 http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
*---
Thanks and Regards,
Bipin Singh*
-- 
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Re: [gmx-users] Re: Manual installation of new analysis tool

2013-04-25 Thread Venkat Reddy

Dear Mark  Junghans,
Thanks for your valuable suggestions.
I have gone through the README file. It says compatibility with 4.5.x
version. I am using 4.5.5. So, I think its not a problem.
@Junghans: I have installed pkg-config  in fact the $ pkg-config --libs
libgmx returns
   the expected output; -lgmx -lm

Here I am sending you the README file as attachment. Please go through it.
If needed, I am happy to provide the code also.

Thanks a lot


On Fri, Apr 26, 2013 at 4:21 AM, Christoph Junghans jungh...@votca.orgwrote:

  Date: Thu, 25 Apr 2013 22:57:55 +0200
  From: Mark Abraham mark.j.abra...@gmail.com
  Subject: Re: [gmx-users] Manual installation of new analysis tool
  To: Discussion list for GROMACS users gmx-users@gromacs.org
  Message-ID:
  CAMNuMAT=tt7EJxdngFaVCK=
 4wko947kc_y7s_gsyrxg8nms...@mail.gmail.com
  Content-Type: text/plain; charset=ISO-8859-1
 
  On Wed, Apr 24, 2013 at 8:14 AM, Venkat Reddy venkat...@gmail.com
 wrote:
 
  Dear all,
  I have got  an analysis tool for analyzing membrane density from Dr.Luca
  monticelli. I have followed the installation instructions as given.
 
  1) First thing is to load GROMACS
 $ *source /usr/local/gromacs/bin/GMXRC*
  2) Enter the source directory of the program then make
 $ cd g_mydensity
 $ make
  According to the instructions, it should create an executable
  *g_mydensity*
  but I am getting the following errors
 
  *cc `pkg-config --libs libgmx`  g_mydensity.o matrix.o distances.o
 
 
  Looks like his Makefile is relying on valid pkg-config registration. I've
  no idea for what GROMACS versions under what conditions pkg-config
 actually
  works, but I suggest you follow his instructions really precisely, and/or
  contact him to resolve any doubtful points.
 I added the pkg-config support with version 4.0.7 if I remember correctly.
 Without knowing further details, two things come to my mind:
 0.) [Trivial] Make sure that pkg-config is actually installed.
 1.) Try if
 $ pkg-config --libs libgmx
 returns some useful output like -lgmx -lm. If not, you might need to
 set PKG_CONFIG_PATH to ${GMXLDLIB}/pkgconfig, but normally GMXRC does
 that for you automatically.
 2.) Some functions in libgmx have been renamed/changed in the
 development from 4.0 to 4.5 to 4.6, so you might actually need to
 change the code, or use the same version as Dr.Luca Monticelli.

 Cheers,

 Christoph


 
  Mark
 
 
  dist_mode.o grid_mode.o   -o g_mydensity*
  *g_mydensity.o: In function `gmx_log2':*
  *g_mydensity.c:(.text+0xa8): undefined reference to `log'*
  *g_mydensity.o: In function `gmx_invsqrt':*
  *g_mydensity.c:(.text+0xf2): undefined reference to
 `gmx_invsqrt_exptab'*
  *g_mydensity.c:(.text+0x101): undefined reference to
  `gmx_invsqrt_fracttab'*
  *g_mydensity.o: In function `matrix_convert':*
  *g_mydensity.c:(.text+0x381): undefined reference to `cos'*
  *g_mydensity.c:(.text+0x3ad): undefined reference to `sin'*
  *g_mydensity.c:(.text+0x3da): undefined reference to `cos'*
  *g_mydensity.c:(.text+0x403): undefined reference to `cos'*
  *g_mydensity.c:(.text+0x416): undefined reference to `cos'*
  *g_mydensity.c:(.text+0x429): undefined reference to `cos'*
  *g_mydensity.c:(.text+0x447): undefined reference to `sin'*
  *g_mydensity.c:(.text+0x4ad): undefined reference to `sqrt'*
  *g_mydensity.o: In function `get_electrons':*
  *g_mydensity.c:(.text+0x527): undefined reference to `ffopen'*
  *g_mydensity.c:(.text+0x564): undefined reference to `gmx_fatal'*
  *g_mydensity.c:(.text+0x5b6): undefined reference to `gmx_fatal'*
  *g_mydensity.c:(.text+0x600): undefined reference to `gmx_fatal'*
  *g_mydensity.c:(.text+0x62e): undefined reference to `save_calloc'*
  *g_mydensity.c:(.text+0x68d): undefined reference to `gmx_fatal'*
  *g_mydensity.c:(.text+0x6eb): undefined reference to `gmx_fatal'*
  *g_mydensity.c:(.text+0x74f): undefined reference to `ffclose'*
  *g_mydensity.o: In function `center_coords':*
  *g_mydensity.c:(.text+0x88f): undefined reference to `calc_box_center'*
  *g_mydensity.o: In function `calc_electron_density':*
  *g_mydensity.c:(.text+0x945): undefined reference to `gmx_fatal'*
  *g_mydensity.c:(.text+0x973): undefined reference to `read_first_x'*
  *g_mydensity.c:(.text+0x9a0): undefined reference to `gmx_fatal'*
  *g_mydensity.c:(.text+0xa38): undefined reference to `save_calloc'*
  *g_mydensity.c:(.text+0xa81): undefined reference to `save_calloc'*
  *g_mydensity.c:(.text+0xac1): undefined reference to `save_calloc'*
  *g_mydensity.c:(.text+0xaf6): undefined reference to `gmx_rmpbc_init'*
  *g_mydensity.c:(.text+0xb18): undefined reference to `set_pbc'*
  *g_mydensity.c:(.text+0xb38): undefined reference to `gmx_rmpbc'*
  *g_mydensity.c:(.text+0xe0b): undefined reference to `read_next_x'*
  *g_mydensity.c:(.text+0xe1e): undefined reference to `gmx_rmpbc_done'*
  *g_mydensity.c:(.text+0xe29): undefined reference to `close_trj'*
  *g_mydensity.c:(.text+0xecc): undefined reference to `save_free'*
  *g_mydensity.o: In

Re: [gmx-users] Re: Martini with PME, temp two low (ABEL Stephane 175950)