[gmx-users] Problems with g_mmpbsa

[Mishelle Oña]

Hi, I am using g_mmpbsa tool for calculate the solvation energy of molecule. 
From the paper Kumari et al (2014) g_mmpbsa - A GROMACS tool for 
high-throughput MM-PBSA calculations. J. Chem. Inf. Model.54:1951-1962. I 
understand that solvation energy is the sum of polar and nonpolar energies so I 
start calculating the polar component with this command: g_mmpbsa -f 
sinagua.trr -s topol.tpr -i mmpbsa.mdp -n index.ndx -nomme -pbsa -pol polar.xvg 
-nodiff It started to appear something like calculation 1- calcultation 
2-calcultation 3- calcultation 4 and it repeats over and over again. I don´t 
have much experience with this tool. Could you tell me how long it takes to do 
an average calculation with this tool?. Also I want to know if it is normal 
that the tool repeats calculation 1- calcultation 2-calcultation 3- 
calcultation 4 over and over again.  
-- 
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Re: [gmx-users] trajectory file

[Alexey Shvetsov]

Timofey Tyugashev писал 15-12-2015 08:41:
04.12.2015 14:43, gromacs.org_gmx-users-requ...@maillist.sys.kth.se 
пишет:
I ran the production MD and got the trajectory file (xtcformat) but as 
I?m new to MD I don?t know how to visualize it. I opened it withvmd 
and it could read the atoms and frames but didn?t show anything when 
playingthe frames. I don?t know whether another program can do it or 
my xtc is notcorrect.

You can also read GROMACS trajectories with PyMOL. It offers quite
nice visualisation options.
Use 'load' command to load the coordinate file first, then load the
trajectory itself using 'load_traj' command.


Only problem with pymol is that it eats very large amount of memory. I 
cannot evel load trajectory of large nucleoprotein complex (~200k atoms 
for complex itself without solvent) if it has ~1000 frames on 
workstation with 64G ram.


--
Best Regards,
Alexey 'Alexxy' Shvetsov, PhD
Department of Molecular and Radiation Biophysics
FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
Leningrad region, Gatchina, Russia
mailto:alexx...@gmail.com
mailto:ale...@omrb.pnpi.spb.ru
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Re: [gmx-users] amber force field ff12SB and ff14SB for gromacs uploaded

[Szilárd Páll]

On Tue, Dec 15, 2015 at 7:52 PM, Man Hoang Viet  wrote:

> Hi Alexey,
>
> Thank you for your interesting in my force field conversion. Below content
> is how I do implement the force fields step by step, which you may follow
> to do double check my work.
>
> I. Get original ff12SB force field from Ambertool15 (free). After untar it
> you will have folder amber14, the directory amber14/dat/leap contains all
> the force field information.
>
> I.1. look at file amber14/dat/leap/cmd/leaprc.ff12SB you will see some
> below lines:
> #
> #   Load the main parameter set.
> #
> parm10 = loadamberparams parm10.dat
> frcmod12SB = loadamberparams frcmod.ff12SB
> #
> #   Load main chain and terminating amino acid libraries, nucleic acids
> #
> loadOff amino12.lib
> loadOff aminoct12.lib
> loadOff aminont12.lib
> loadOff nucleic12.lib
> ##
> It means ff12SB will use parameter from parm10.dat and the modified
> parameters from frcmod.ff12SB (you can find these two files in
> amber14/dat/leap/parm). The files *.lib are stored in amber14/dat/leap/lib
> and they contain information of residues such as number of atoms,
> atomtypes, charge ...
>
> I.2. Before doing conversion, we need understand the information in above
> files (parm10.dat, ...). The following link will help us on that
> http://ambermd.org/formats.html
>
> II. Do convert
> Because ff12SB is developed from amber99SB, I use amber99SB as template
> and modify to get ff12SB.
> The information (atom, bond, angle, improper and dihedrals) for ffbond.itp
> and ffnonbond.itp will get from parm10.dat and frcmod.ff12SB. Note that if
> the same atom (or bonds, angles ..) shows in both the two files, we will
> only keep the ones in frcmod.ff12SB.
> The files amin*lib will be used to correct aminoacids.rtp and, while
> nucleic12.lib for dna.rtp and rna.rtp.
>
> II.1. Convert atom types (adding new atom type to ffnonbond.itp)
> The first part in parm10.dat and frcmod.ff12SB introduced atomtypes and
> their mass, while the last part give us parameters for 6-12 interaction.
>
> The last part of parm10.dat:
> ...
> N   NA  N2  N*  NC  NB  NT  NY
> C*  CA  CB  CC  CD  CK  CM  CN  CQ  CR  CV  CW  CY  CZ  CP  CS
>
> MOD4  RE
>   H   0.6000  0.0157!Ferguson base pair geom.
>   ...
>   N   1.8240  0.1700 OPLS
>   ...
> END
>
> The line "N   NA  N2  N*  NC  NB  NT  NY" indicates all those atoms share
> the same parameters. It is similar for the line "C*  CA  CB  CC  CD  CK
> CM  CN  CQ  CR  CV  CW  CY  CZ  CP  CS"
> The line "N   1.8240  0.1700" means van der Waals radius  and
> epsilon of atom N are 1.8240 ‎Å and 0.1700 kcal/mol, respectively ---> in
> gromacs (ffnonbond.itp) atom N will has
> sigma=1.7818*1.8240*10^1=3.25000e-1, and epsilon=0.1700*4.184=7.11280e-1
> (kJ/mol). The constant 1.7818=2/{2^(1/6)}.
> By this way, it is easy to add some new atomtypes such as CX, 2C, 3C ..
>
> II.2. Convert bonds and angles (ffbond.itp)
> This is a simple work, because we only need consider unit from kcal in
> amber to kJ in gromacs for the "harmonic force constants".
>
> II.3. Convert impropers
> in AMBER:
> ;i j k l PK Phase  PN
> CA-CA-CA-OH 1.1  180.  2.
>
> in gromacs: a improper is dihedraltype 4
> ;i   j   k   lfunc  phase  kd pn
> CA  CA  CA  OH   4  180.00 4.60240 2
>
> for improper, gromacs define as dihedral by function type 4 and
> kd=PK*4.184
>
>
> II.4. Convert dihedrals:
>
> Some examples for dihedrals in amber:
> ;i j k lIDIVF   PK PHASEPN
>
> X -CI-OS-X31.150 0.0 3.
> X -CX-N3-X91.40  0.0 3.
> X -C4-N*-X47.40180.0 2.
>
> CX-2C-S -S20.386   137.8-4.Cyx chi2
> CX-2C-S -S20.33712.0-3.
> CX-2C-S -S21.166   -40.1-2.
> CX-2C-S -S21.389  -112.7 1.
>
> 2C-S -S -2C   10.19332.5-4.Cyx disulf
> 2C-S -S -2C   10.957-0.5-3.
> 2C-S -S -2C   14.542 1.5-2.
> 2C-S -S -2C   10.543   -25.0 1.
>
> convert in to gromacs
> ;i   j   k   lfunc  phase  kd pn
>
>  X   CI  OS  X 9 0.0  1.60387 3
>  X   CX  N3  X 9 0.0  0.65084 3
>  X   C4  N*  X 9   180.0  7.74040 2
>
>  CX  2C  2C  S 986.9  0.63178 4
>  CX  2C  2C  S 979.7  0.63178 3
>  CX  2C  2C  S 9 8.3  0.99579 2
>  CX  2C  2C  S 9-3.8  1.63594 1
>
>  2C  S   S   2C932.5  0.80751 4
>  2C  S   S   2C9-0.5  4.00409 3
>  2C  S   S   2C9 1.5 19.00373 2
>  2C  S   S   2C9   -25.0  2.27191 1
>
> In gromacs dihedrals func=9, kd=PK*4.184/IDIVF.
>
> II.5. 

Re: [gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

[Justin Lemkul]

On 12/15/15 8:42 AM, NISHA Prakash wrote:

Hi all,

I am trying to simulate a protein using similar parameters as in the
tutorial - Protein ligand by Justin Lemkul.

I am facing a problem wherein the protein simulation is exploding only in
this version - Gromacs-v5.0.5 but not in the older version Gromacs-v4.5.4.

The warning message is as follows

---
There were 4 inconsistent shifts. Check your topology

Steepest Descents:
Tolerance (Fmax)   =  1.0e+03
Number of steps=5

WARNING: Listed nonbonded interaction between particles 1312 and 1315
at distance 4.728 which is larger than the table limit 2.000 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

ATOM   1312  O   TYR A 207
ATOM   1315  CD1 TYR A 207
-



---
em_real.mdp file

; LINES STARTING WITH ';' ARE COMMENTS
title = Minimization ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform
energygrps = Protein ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long range
forces
cutoff-scheme   = Verlet
ns_type= grid ; Method to determine neighbor list (simple, grid)
rlist= 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype= PME ; Treatment of long range electrostatic interactions
rcoulomb= 1.0 ; long range electrostatic cut-off
rvdw= 1.0 ; long range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions




The initial minimization step itself fails.


If minimization fails, you have a problem with the topology or coordinates. 
Perhaps you got a bit lucky with some quirk of an algorithmic difference in the 
old version that is failing here.


-Justin


I have tried to simulate a minimized structure as well, I still encounter
the same problem.

I would appreciate any help in this regard.
I would also like to know if this means, that the results from the older
version of gromacs reliable?

Thanking you in anticipation

Nisha



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Calculation of polar energy question

[Justin Lemkul]

On 12/15/15 2:53 PM, Mishelle Oña wrote:

Hi, I am using g_mmpbsa tool for calculate the solvation energy of molecule. 
From the paper Kumari et al (2014) g_mmpbsa - A GROMACS tool for 
high-throughput MM-PBSA calculations. J. Chem. Inf. Model.54:1951-1962. I 
understand that solvation energy is the sum of polar and nonpolar energies so I 
start calculating the polar component with this command: g_mmpbsa -f 
sinagua.trr -s topol.tpr -i mmpbsa.mdp -n index.ndx -nomme -pbsa -pol polar.xvg 
-nodiff It started to appear something like calculation 1- calcultation 
2-calcultation 3- calcultation 4 and it repeats over and over again. I don´t 
have much experience with this tool. Could you tell me how long it takes to do 
an average calculation with this tool?. Also I want to know if it is normal 
that the tool repeats calculation 1- calcultation 2-calcultation 3- 
calcultation 4 over and over again.
Please, I need your help


Perhaps you should try contacting the author or posting to the g_mmpbsa help 
forum (https://groups.google.com/forum/#!forum/g_mmpbsa) rather than continually 
post here.  If you're not getting replies, it's because no one knows the answer.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] amber force field ff12SB and ff14SB for gromacs uploaded

[Man Hoang Viet]

Hi Alexey,

Thank you for your interesting in my force field conversion. Below content
is how I do implement the force fields step by step, which you may follow
to do double check my work.

I. Get original ff12SB force field from Ambertool15 (free). After untar it
you will have folder amber14, the directory amber14/dat/leap contains all
the force field information.

I.1. look at file amber14/dat/leap/cmd/leaprc.ff12SB you will see some
below lines:
#
#   Load the main parameter set.
#
parm10 = loadamberparams parm10.dat
frcmod12SB = loadamberparams frcmod.ff12SB
#
#   Load main chain and terminating amino acid libraries, nucleic acids
#
loadOff amino12.lib
loadOff aminoct12.lib
loadOff aminont12.lib
loadOff nucleic12.lib
##
It means ff12SB will use parameter from parm10.dat and the modified
parameters from frcmod.ff12SB (you can find these two files in
amber14/dat/leap/parm). The files *.lib are stored in amber14/dat/leap/lib
and they contain information of residues such as number of atoms,
atomtypes, charge ...

I.2. Before doing conversion, we need understand the information in above
files (parm10.dat, ...). The following link will help us on that
http://ambermd.org/formats.html

II. Do convert
Because ff12SB is developed from amber99SB, I use amber99SB as template
and modify to get ff12SB.
The information (atom, bond, angle, improper and dihedrals) for ffbond.itp
and ffnonbond.itp will get from parm10.dat and frcmod.ff12SB. Note that if
the same atom (or bonds, angles ..) shows in both the two files, we will
only keep the ones in frcmod.ff12SB.
The files amin*lib will be used to correct aminoacids.rtp and, while
nucleic12.lib for dna.rtp and rna.rtp.

II.1. Convert atom types (adding new atom type to ffnonbond.itp)
The first part in parm10.dat and frcmod.ff12SB introduced atomtypes and
their mass, while the last part give us parameters for 6-12 interaction.

The last part of parm10.dat:
...
N   NA  N2  N*  NC  NB  NT  NY
C*  CA  CB  CC  CD  CK  CM  CN  CQ  CR  CV  CW  CY  CZ  CP  CS

MOD4  RE
  H   0.6000  0.0157!Ferguson base pair geom.
  ...
  N   1.8240  0.1700 OPLS
  ...
END

The line "N   NA  N2  N*  NC  NB  NT  NY" indicates all those atoms share
the same parameters. It is similar for the line "C*  CA  CB  CC  CD  CK 
CM  CN  CQ  CR  CV  CW  CY  CZ  CP  CS"
The line "N   1.8240  0.1700" means van der Waals radius  and
epsilon of atom N are 1.8240 ‎Å and 0.1700 kcal/mol, respectively ---> in
gromacs (ffnonbond.itp) atom N will has
sigma=1.7818*1.8240*10^1=3.25000e-1, and epsilon=0.1700*4.184=7.11280e-1
(kJ/mol). The constant 1.7818=2/{2^(1/6)}.
By this way, it is easy to add some new atomtypes such as CX, 2C, 3C ..

II.2. Convert bonds and angles (ffbond.itp)
This is a simple work, because we only need consider unit from kcal in
amber to kJ in gromacs for the "harmonic force constants".

II.3. Convert impropers
in AMBER:
;i j k l PK Phase  PN
CA-CA-CA-OH 1.1  180.  2.

in gromacs: a improper is dihedraltype 4
;i   j   k   lfunc  phase  kd pn
CA  CA  CA  OH   4  180.00 4.60240 2

for improper, gromacs define as dihedral by function type 4 and
kd=PK*4.184


II.4. Convert dihedrals:

Some examples for dihedrals in amber:
;i j k lIDIVF   PK PHASEPN

X -CI-OS-X31.150 0.0 3.
X -CX-N3-X91.40  0.0 3.
X -C4-N*-X47.40180.0 2.

CX-2C-S -S20.386   137.8-4.Cyx chi2
CX-2C-S -S20.33712.0-3.
CX-2C-S -S21.166   -40.1-2.
CX-2C-S -S21.389  -112.7 1.

2C-S -S -2C   10.19332.5-4.Cyx disulf
2C-S -S -2C   10.957-0.5-3.
2C-S -S -2C   14.542 1.5-2.
2C-S -S -2C   10.543   -25.0 1.

convert in to gromacs
;i   j   k   lfunc  phase  kd pn

 X   CI  OS  X 9 0.0  1.60387 3
 X   CX  N3  X 9 0.0  0.65084 3
 X   C4  N*  X 9   180.0  7.74040 2

 CX  2C  2C  S 986.9  0.63178 4
 CX  2C  2C  S 979.7  0.63178 3
 CX  2C  2C  S 9 8.3  0.99579 2
 CX  2C  2C  S 9-3.8  1.63594 1

 2C  S   S   2C932.5  0.80751 4
 2C  S   S   2C9-0.5  4.00409 3
 2C  S   S   2C9 1.5 19.00373 2
 2C  S   S   2C9   -25.0  2.27191 1

In gromacs dihedrals func=9, kd=PK*4.184/IDIVF.

II.5. Correct amino acids, dna and rna by new atoms type.
In this part, I have compared residues in gromacs to residues in amber and
changed some atomtypes to make sure thay are the same in amber and
gromacs.

The work for the ff14SB conversion is similar.

I have written some codes (scripts and Fortran) to 

[gmx-users] Calculation of polar energy question

[Mishelle Oña]

Hi, I am using g_mmpbsa tool for calculate the solvation energy of molecule. 
From the paper Kumari et al (2014) g_mmpbsa - A GROMACS tool for 
high-throughput MM-PBSA calculations. J. Chem. Inf. Model.54:1951-1962. I 
understand that solvation energy is the sum of polar and nonpolar energies so I 
start calculating the polar component with this command: g_mmpbsa -f 
sinagua.trr -s topol.tpr -i mmpbsa.mdp -n index.ndx -nomme -pbsa -pol polar.xvg 
-nodiff It started to appear something like calculation 1- calcultation 
2-calcultation 3- calcultation 4 and it repeats over and over again. I don´t 
have much experience with this tool. Could you tell me how long it takes to do 
an average calculation with this tool?. Also I want to know if it is normal 
that the tool repeats calculation 1- calcultation 2-calcultation 3- 
calcultation 4 over and over again. 
Please, I need your help
Thanks
  
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Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

This is a frequently occurring task, which you would probably learn about
in doing some of the many online tutorials. Did you?

Mark

On Tue, Dec 15, 2015 at 5:33 PM saranya  wrote:

> Hello sir,
>   i want to extract the final pdb file for each ns, can you please
> explain how to extract the pdb files.
>
>
> With Regards,
>
> *Saranya Vasudevan,*
>
> *Research Scholar,*
>
> *Molecular Quantum Mechanics Laboratory,*
>
> *Department of Physics,*
>
> *Bharathiar University,*
>
> *Coimbatore-46*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Viscosity of water from gmx tcaf

[Gmx QA]

Dear users

I am trying to teach myself how to calculate the viscosity of different
simulations from gmx tcaf, and to that end I made a test system with a box
of about 4000 water molecules, so that I can see if I can get a viscosity
that matches that of water.

I have read some mails on this list, and in particular the Berk Hess paper
about various methods to calculate viscosity in gromacs, but I have some
additional questions.

>From the help-text for gmx tcaf:
The k-dependent viscosities in the -ov file should be fitted to eta(k) =
eta_0
(1 - a k^2) to obtain the viscosity at infinite wavelength.

This is my command line for running gmx tcaf:
$ gmx tcaf -f run.trr -s run.tpr -ov

which gives me the visc_k.xvg file.

I then tried to fit the data (per above) using xmgrace to y = a0 * (1 - a1
* y * y), and get a0 = 0.41*10^-3 kg /m*s, which after unit conversion
seems to be too low? (wikipedia says viscosity of water is 0.001 kg /m *s.

On the other hand, gmx tcaf also says:

When the box is cubic, one can use the option -oc, which averages the TCAFs
over all k-vectors with the same length. This results in more accurate
TCAFs. Both the cubic TCAFs and fits are written to -oc The cubic eta
estimates are also written to -ov.

Since I have a cubic box, I run
$ gmx tcaf -f run.trr -s run.tpr -ov -oc

which gives me another visc_k,xvg file with some (fitted?) data in it. What
is this data?
The following is also printed to stdout

Averaged over k-vectors:
k  1.273  tau  1.860  Omega  1.790  eta  0.14901 10^-3 kg/(m s)
k  1.801  tau  1.133  Omega  2.061  eta  0.14087 10^-3 kg/(m s)
k  2.206  tau  0.420  Omega  0.799  eta  0.09827 10^-3 kg/(m s)
k  2.547  tau  0.340  Omega  0.599  eta  0.06810 10^-3 kg/(m s)

Does gromacs somehow already compute the viscosity at "infinite
wavelength"?, or am i missing something.

I'd really, really appreciate some help here.

Best
/PK
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Re: [gmx-users] amber force field ff12SB and ff14SB for gromacs uploaded

[Michael Shirts]

> Yes, I just try to show to Alexey Shvetsov or some gromas users who want
> to do check the conversion.

The issue is that the hardest and most time consuming part is not the
conversion itself, but the testing.  Without the testing, the
conversion isn't that useful.  I appreciate the work you've done, but
the hard part is still ahead.

> It is too much thing to post for the detail of
> residue comparing. I agree with your suggestion about testing. I will try
> to do test and report it as soon as possible.

The information here gives a good example of good testing.

http://ffamber.cnsm.csulb.edu/ffamber.php

In fact, you could offer your files to Prof. Sorin and see if he wants
to collaborate on testing.

> Here I really want other
> gromacs users do check my conversion and take apart the testing to make
> the conversion completely successful. It will give us more freedom in
> doing with GROMACS.
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Re: [gmx-users] amber force field ff12SB and ff14SB for gromacs uploaded

[Man Hoang Viet]

Hi,

> Date: Tue, 15 Dec 2015 13:55:08 -0500
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] amber force field ff12SB and ff14SB for
>   gromacs uploaded
> Message-ID: <5670620c.6040...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 12/15/15 1:52 PM, Man Hoang Viet wrote:

> The concern is less about the method of conversion; these types of
> programs are
> reasonably straightforward to write.  The concern is always that the
> energies
> and forces calculated in one program match the other.  The simplest thing
> to do
> is run some single-point energy evaluations in AMBER and GROMACS.  If they
> match, your conversion is successful.  If they don't, you have a problem
> with
> the integrity of the GROMACS files.  You say above that you "make sure
> that they
> are the same in AMBER and GROMACS" but you don't specify what that means.
> Visual inspection of the contents?  Or actual quantitative assessment?
>
> -Justin
>

Yes, I just try to show to Alexey Shvetsov or some gromas users who want
to do check the conversion. It is too much thing to post for the detail of
residue comparing. I agree with your suggestion about testing. I will try
to do test and report it as soon as possible. Here I really want other
gromacs users do check my conversion and take apart the testing to make
the conversion completely successful. It will give us more freedom in
doing with GROMACS.


> Date: Tue, 15 Dec 2015 20:36:52 +0100
> From: Szil?rd P?ll 
> To: Discussion list for GROMACS users 
> Cc: Discussion list for GROMACS users

> Why is documentation not important, could you elaborate?

I just mean it does not effect on gromacs running. I know it is very
important to authorized information.

>
> Note that the Makefiles are outdated too, I suggest either fixing them or
> removing them.

Thank you for your comment, I fixed it.

> Plus, you seem to have left no contact information in the tarball either
> which (together with the unclear verification process), I'd say, makes the
> FF port risky to use.

I work alone in the conversion that why I wish other users do check and
test the FF together. I hope coming tests will remove the risky and we
will have the new FF in GROMACS.

Viet Man


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Re: [gmx-users] Errors from alchemical_analysis.py from analyzing .xvg files

[Michael Shirts]

You should file an issue on the alchemical-analysis issue tracker.

https://github.com/MobleyLab/alchemical-analysis

On Tue, Dec 15, 2015 at 8:35 PM, Nathan K Houtz  wrote:
> Hello,
>
>
> This request is related to python programs used for analyzing gromacs 
> outputs, not gromacs itself. If there is a more appropriate forum for this 
> question, let me know and I apologize for posting here.
>
>
> I have performed a bunch of thermodynamic-integration simulations for liquid 
> water in Gromacs, and am trying to analyze the .xvg files with the python 
> script mentioned in the ethanol solvation tutorial: 
> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy
>  (I think the tutorial is out of date - the python script is now called 
> alchemical_analysis.py and I think it is called with slightly different 
> flags). It may be relevant that I'm using Windows 10 and installed Anaconda2 
> (64 bit) with the gui installer and then pymbar through Anaconda2 before 
> downloading alchemical-analysis-master.
>
>
> In a Windows command prompt, I entered:
>
>>python alchemical_analysis.py -d C:\\ -t 200 -p 1 -v  > results
>
>
> This is the result:
>
> Traceback (most recent call last):
>   File "alchemical_analysis.py", line 1224, in 
> main()
>   File "alchemical_analysis.py", line 1166, in main
> nsnapshots, lv, dhdlt, u_klt = parser_gromacs.readDataGromacs(P)
>   File 
> "C:\<...>\alchemical-analysis-master\alchemical_analysis\parser_gromacs.py", 
> line 187, in readDataGromacs
> fs = sorted(fs, key=F.sortedHelper)
>   File 
> "C:\<...>\alchemical-analysis-master\alchemical_analysis\parser_gromacs.py", 
> line 48, in sortedHelper
> self.state = l[0] = int(l[0]) # Will be of use for selective MBAR 
> analysis.
> IndexError: list index out of range
>
>
> where <...> is just the directory to which I downloaded 
> alchemical-analysis-master. I don't understand the error and cannot find help 
> for it online. In the directory where I have the .xvg files, all the files 
> are simply named integers: 0.xvg, 1.xvg, 2.xvg,  20.xvg, and there are no 
> other files in that folder. I don't want to tinker with the python code and 
> accidentally mess something up. Am I calling the script correctly? Could it 
> be the operating system (Windows vs. Linux)? I might be able to get on a 
> Linux machine if it would help.
>
>
> Thanks very much,
>
> N. H.
>
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Re: [gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

[NISHA Prakash]

Dear Justin,

I am simulating a protein ligand complex. The protein co-ordinate file that
I have taken is an output of the simulation of the protein alone in
Gromacs-v5.0.5. The topology and the co-ordinates are fine. I am still
facing this problem wherein I get the LINCS warning for only the protein
atoms. The ligand also is fine.
Like I mentioned before, I do not have this problem when I use the
Gromacs-4.5.4 where I have used the same co-ordinate file with different
ligands and same parameter file.

Kindly let me know how to resolve the issue.

Thanking you in anticipation.

Nisha




On Wed, Dec 16, 2015 at 12:26 AM, Justin Lemkul  wrote:

>
>
> On 12/15/15 8:42 AM, NISHA Prakash wrote:
>
>> Hi all,
>>
>> I am trying to simulate a protein using similar parameters as in the
>> tutorial - Protein ligand by Justin Lemkul.
>>
>> I am facing a problem wherein the protein simulation is exploding only in
>> this version - Gromacs-v5.0.5 but not in the older version Gromacs-v4.5.4.
>>
>> The warning message is as follows
>>
>> ---
>> There were 4 inconsistent shifts. Check your topology
>>
>> Steepest Descents:
>> Tolerance (Fmax)   =  1.0e+03
>> Number of steps=5
>>
>> WARNING: Listed nonbonded interaction between particles 1312 and 1315
>> at distance 4.728 which is larger than the table limit 2.000 nm.
>>
>> This is likely either a 1,4 interaction, or a listed interaction inside
>> a smaller molecule you are decoupling during a free energy calculation.
>> Since interactions at distances beyond the table cannot be computed,
>> they are skipped until they are inside the table limit again. You will
>> only see this message once, even if it occurs for several interactions.
>>
>> IMPORTANT: This should not happen in a stable simulation, so there is
>> probably something wrong with your system. Only change the table-extension
>> distance in the mdp file if you are really sure that is the reason.
>> 
>> ATOM   1312  O   TYR A 207
>> ATOM   1315  CD1 TYR A 207
>> -
>>
>>
>>
>> ---
>> em_real.mdp file
>>
>> ; LINES STARTING WITH ';' ARE COMMENTS
>> title = Minimization ; Title of run
>>
>> ; Parameters describing what to do, when to stop and what to save
>> integrator = steep ; Algorithm (steep = steepest descent minimization)
>> emtol = 1000.0   ; Stop minimization when the maximum force < 10.0 kJ/mol
>> emstep  = 0.01  ; Energy step size
>> nsteps = 5   ; Maximum number of (minimization) steps to perform
>> energygrps = Protein ; Which energy group(s) to write to disk
>>
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> nstlist= 1; Frequency to update the neighbor list and long range
>> forces
>> cutoff-scheme   = Verlet
>> ns_type= grid ; Method to determine neighbor list (simple, grid)
>> rlist= 1.0 ; Cut-off for making neighbor list (short range forces)
>> coulombtype= PME ; Treatment of long range electrostatic interactions
>> rcoulomb= 1.0 ; long range electrostatic cut-off
>> rvdw= 1.0 ; long range Van der Waals cut-off
>> pbc= xyz ; Periodic Boundary Conditions
>>
>>
>> 
>>
>> The initial minimization step itself fails.
>>
>
> If minimization fails, you have a problem with the topology or
> coordinates. Perhaps you got a bit lucky with some quirk of an algorithmic
> difference in the old version that is failing here.
>
> -Justin
>
> I have tried to simulate a minimized structure as well, I still encounter
>> the same problem.
>>
>> I would appreciate any help in this regard.
>> I would also like to know if this means, that the results from the older
>> version of gromacs reliable?
>>
>> Thanking you in anticipation
>>
>> Nisha
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
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> * Please search the archive at
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> posting!
>
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Re: [gmx-users] X11 forwarding!

[Mark Abraham]

Hi,

Please ask questions unrelated to GROMACS in a more appropriate forum.

Mark

On Tue, Dec 15, 2015 at 11:57 PM Elsaid Younes  wrote:

> Hi all,
>
>
> I can not do ssh over X, although my sshd-config is:
>
>
> # Package generated configuration file
> # See the sshd_config(5) manpage for details
>
> # What ports, IPs and protocols we listen for
> Port 22
> # Use these options to restrict which interfaces/protocols sshd will bind
> to
> #ListenAddress ::
> #ListenAddress 0.0.0.0
> Protocol 2
> # HostKeys for protocol version 2
> HostKey /etc/ssh/ssh_host_rsa_key
> HostKey /etc/ssh/ssh_host_dsa_key
> HostKey /etc/ssh/ssh_host_ecdsa_key
> HostKey /etc/ssh/ssh_host_ed25519_key
> #Privilege Separation is turned on for security
> UsePrivilegeSeparation yes
>
> # Lifetime and size of ephemeral version 1 server key
> KeyRegenerationInterval 3600
> ServerKeyBits 1024
>
> # Logging
> SyslogFacility AUTH
> LogLevel INFO
>
> # Authentication:
> LoginGraceTime 120
> PermitRootLogin without-password
> StrictModes yes
>
> RSAAuthentication yes
> PubkeyAuthentication yes
> #AuthorizedKeysFile %h/.ssh/authorized_keys
>
> # Don't read the user's ~/.rhosts and ~/.shosts files
> IgnoreRhosts yes
> # For this to work you will also need host keys in /etc/ssh_known_hosts
> RhostsRSAAuthentication no
> # similar for protocol version 2
> HostbasedAuthentication no
> # Uncomment if you don't trust ~/.ssh/known_hosts for
> RhostsRSAAuthentication
> #IgnoreUserKnownHosts yes
>
> # To enable empty passwords, change to yes (NOT RECOMMENDED)
> PermitEmptyPasswords no
>
> # Change to yes to enable challenge-response passwords (beware issues with
> # some PAM modules and threads)
> ChallengeResponseAuthentication no
>
> # Change to no to disable tunnelled clear text passwords
> #PasswordAuthentication yes
>
> # Kerberos options
> #KerberosAuthentication no
> #KerberosGetAFSToken no
> #KerberosOrLocalPasswd yes
> #KerberosTicketCleanup yes
>
> # GSSAPI options
> #GSSAPIAuthentication no
> #GSSAPICleanupCredentials yes
> X11UseLocalHost no
> X11Forwarding yes
> X11DisplayOffset 10
> PrintMotd no
> PrintLastLog yes
> TCPKeepAlive yes
> #UseLogin no
>
> #MaxStartups 10:30:60
> #Banner /etc/issue.net
>
> # Allow client to pass locale environment variables
> AcceptEnv LANG LC_*
>
> Subsystem sftp /usr/lib/openssh/sftp-server
>
> # Set this to 'yes' to enable PAM authentication, account processing,
> # and session processing. If this is enabled, PAM authentication will
> # be allowed through the ChallengeResponseAuthentication and
> # PasswordAuthentication.  Depending on your PAM configuration,
> # PAM authentication via ChallengeResponseAuthentication may bypass
> # the setting of "PermitRootLogin without-password".
> # If you just want the PAM account and session checks to run without
> # PAM authentication, then enable this but set PasswordAuthentication
> # and ChallengeResponseAuthentication to 'no'.
> UsePAM yes
>
>
>
>
>
> Typing xauth info shows:
>
> File new: yes
> File locked:  no
> Number of entries:0
> Changes honored:  yes
> Changes made: no
> Current input:(argv):1
>
> Also I can't use scp. Any ideas?
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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[gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

[NISHA Prakash]

Hi all,

I am trying to simulate a protein using similar parameters as in the
tutorial - Protein ligand by Justin Lemkul.

I am facing a problem wherein the protein simulation is exploding only in
this version - Gromacs-v5.0.5 but not in the older version Gromacs-v4.5.4.

The warning message is as follows

---
There were 4 inconsistent shifts. Check your topology

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=5

WARNING: Listed nonbonded interaction between particles 1312 and 1315
at distance 4.728 which is larger than the table limit 2.000 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

ATOM   1312  O   TYR A 207
ATOM   1315  CD1 TYR A 207
-



---
em_real.mdp file

; LINES STARTING WITH ';' ARE COMMENTS
title = Minimization ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform
energygrps = Protein ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long range
forces
cutoff-scheme   = Verlet
ns_type= grid ; Method to determine neighbor list (simple, grid)
rlist= 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype= PME ; Treatment of long range electrostatic interactions
rcoulomb= 1.0 ; long range electrostatic cut-off
rvdw= 1.0 ; long range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions




The initial minimization step itself fails.
I have tried to simulate a minimized structure as well, I still encounter
the same problem.

I would appreciate any help in this regard.
I would also like to know if this means, that the results from the older
version of gromacs reliable?

Thanking you in anticipation

Nisha
-- 
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[gmx-users] X11 forwarding!

[Elsaid Younes]

Hi all,


I can not do ssh over X, although my sshd-config is:


# Package generated configuration file
# See the sshd_config(5) manpage for details

# What ports, IPs and protocols we listen for
Port 22
# Use these options to restrict which interfaces/protocols sshd will bind to
#ListenAddress ::
#ListenAddress 0.0.0.0
Protocol 2
# HostKeys for protocol version 2
HostKey /etc/ssh/ssh_host_rsa_key
HostKey /etc/ssh/ssh_host_dsa_key
HostKey /etc/ssh/ssh_host_ecdsa_key
HostKey /etc/ssh/ssh_host_ed25519_key
#Privilege Separation is turned on for security
UsePrivilegeSeparation yes

# Lifetime and size of ephemeral version 1 server key
KeyRegenerationInterval 3600
ServerKeyBits 1024

# Logging
SyslogFacility AUTH
LogLevel INFO

# Authentication:
LoginGraceTime 120
PermitRootLogin without-password
StrictModes yes

RSAAuthentication yes
PubkeyAuthentication yes
#AuthorizedKeysFile %h/.ssh/authorized_keys

# Don't read the user's ~/.rhosts and ~/.shosts files
IgnoreRhosts yes
# For this to work you will also need host keys in /etc/ssh_known_hosts
RhostsRSAAuthentication no
# similar for protocol version 2
HostbasedAuthentication no
# Uncomment if you don't trust ~/.ssh/known_hosts for RhostsRSAAuthentication
#IgnoreUserKnownHosts yes

# To enable empty passwords, change to yes (NOT RECOMMENDED)
PermitEmptyPasswords no

# Change to yes to enable challenge-response passwords (beware issues with
# some PAM modules and threads)
ChallengeResponseAuthentication no

# Change to no to disable tunnelled clear text passwords
#PasswordAuthentication yes

# Kerberos options
#KerberosAuthentication no
#KerberosGetAFSToken no
#KerberosOrLocalPasswd yes
#KerberosTicketCleanup yes

# GSSAPI options
#GSSAPIAuthentication no
#GSSAPICleanupCredentials yes
X11UseLocalHost no
X11Forwarding yes
X11DisplayOffset 10
PrintMotd no
PrintLastLog yes
TCPKeepAlive yes
#UseLogin no

#MaxStartups 10:30:60
#Banner /etc/issue.net

# Allow client to pass locale environment variables
AcceptEnv LANG LC_*

Subsystem sftp /usr/lib/openssh/sftp-server

# Set this to 'yes' to enable PAM authentication, account processing,
# and session processing. If this is enabled, PAM authentication will
# be allowed through the ChallengeResponseAuthentication and
# PasswordAuthentication.  Depending on your PAM configuration,
# PAM authentication via ChallengeResponseAuthentication may bypass
# the setting of "PermitRootLogin without-password".
# If you just want the PAM account and session checks to run without
# PAM authentication, then enable this but set PasswordAuthentication
# and ChallengeResponseAuthentication to 'no'.
UsePAM yes





Typing xauth info shows:

File new: yes
File locked:  no
Number of entries:0
Changes honored:  yes
Changes made: no
Current input:(argv):1

Also I can't use scp. Any ideas?
-- 
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[gmx-users] Errors from alchemical_analysis.py from analyzing .xvg files

[Nathan K Houtz]

Hello,


This request is related to python programs used for analyzing gromacs outputs, 
not gromacs itself. If there is a more appropriate forum for this question, let 
me know and I apologize for posting here.


I have performed a bunch of thermodynamic-integration simulations for liquid 
water in Gromacs, and am trying to analyze the .xvg files with the python 
script mentioned in the ethanol solvation tutorial: 
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy
 (I think the tutorial is out of date - the python script is now called 
alchemical_analysis.py and I think it is called with slightly different flags). 
It may be relevant that I'm using Windows 10 and installed Anaconda2 (64 bit) 
with the gui installer and then pymbar through Anaconda2 before downloading 
alchemical-analysis-master.


In a Windows command prompt, I entered:

>python alchemical_analysis.py -d C:\\ -t 200 -p 1 -v  > results


This is the result:

Traceback (most recent call last):
  File "alchemical_analysis.py", line 1224, in 
main()
  File "alchemical_analysis.py", line 1166, in main
nsnapshots, lv, dhdlt, u_klt = parser_gromacs.readDataGromacs(P)
  File 
"C:\<...>\alchemical-analysis-master\alchemical_analysis\parser_gromacs.py", 
line 187, in readDataGromacs
fs = sorted(fs, key=F.sortedHelper)
  File 
"C:\<...>\alchemical-analysis-master\alchemical_analysis\parser_gromacs.py", 
line 48, in sortedHelper
self.state = l[0] = int(l[0]) # Will be of use for selective MBAR analysis.
IndexError: list index out of range


where <...> is just the directory to which I downloaded 
alchemical-analysis-master. I don't understand the error and cannot find help 
for it online. In the directory where I have the .xvg files, all the files are 
simply named integers: 0.xvg, 1.xvg, 2.xvg,  20.xvg, and there are no other 
files in that folder. I don't want to tinker with the python code and 
accidentally mess something up. Am I calling the script correctly? Could it be 
the operating system (Windows vs. Linux)? I might be able to get on a Linux 
machine if it would help.


Thanks very much,

N. H.

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