date:20170622

[gmx-users] Which method for choosing concentration is more appropriate

2017-06-22 Thread Apramita Chand

Dear All,
This is a general query regarding solvation of peptide in urea-water.
My method is to place the peptide in the box first, add urea molecules
using g_genbox and then solvate it using water molecules to maintain a
desired concentration.
There can be two approaches to this:
1) I can keep no.of water molecules constant and increase the urea
molecules like 15,30,45 and so on.
Here total number of particles will not remain constant

2) I can keep total number of particles constant. Say I have 999 water
molecules initially and then I add 15 molecules of urea and the system
becomes like 985water-15urea and then subsequently 969water-30urea.
But wouln't the effect on peptide hydration will be biased in terms of
which is actually causing decrease/increase in hydrogen bonding with water:
decrease of water or addition of cosolute?

In many papers, I have seen that the no.of water molecules decreases with
addition of cosolute.
Is there any drawback if  I use the first method?

Yours sincerely
Apramita
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[gmx-users] Regarding creating a itp for molecule from CGenFF

2017-06-22 Thread Dilip H N

Hello all,

I want to simulate methylamine with amino acid misture in CHARMM FF, so i
have created methylamine in mol2 format and created the .itp and .pdb files
from the CGenFF (which creates itp in CHARMM FF for GROMACS). and i have
included it in topology file also as:-  #Include "methylamine.itp", have
solvated the system,
But if i give the command for energy minimization:-
gmx grompp -f em.mdp -c abc.gro -p topol.top -o em.tpr
i am getting the error as

NOTE 1 [file em.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to -1252943664
Generated 85052 of the 85078 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 55198 of the 85078 1-4 parameter combinations

ERROR 1 [file Dimethylamine.itp, line 9]:
  Atomtype 7 not found

How can i solve these error..??
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults

2017-06-22 Thread Qing Lv

I changed the order of .itp file and put the "topol_ATP.itp" ahead of 
protein.itp . However, I got the following errors this time:
Fatal error:
Syntax error - File forcefield.itp, line 6
Last line read:
'  11   no  1.0 1.0'
Found a second defaults directive.

P.S.
My topology file includes ATP, Protein, and Mg2+.  I tried to remove Mg2+ 
(probably inappropriate) but still got the same errors.

Thanks,
Qing

At 2017-06-23 09:46:49, "Qing Lv"  wrote:
>Dear All,
>
>
>I am setting up a simulation of protein-ATP complex. I manually combined the 
>coordinates and topologies of the protein and ATP together, and ran editconf 
>and solvate successfully. However, when I ran grompp, errors occurred:
>Syntax error - File forcefield.itp, line 4
>Last line read:
>'[ defaults ]'
>Invalid order for directive defaults
>
>
>I checked the .itp files I used and did not find "[ defaults ]" pattern. How 
>to fix it?
>Thanks,
>Qing
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[gmx-users] 5-letter atom names in topology files

2017-06-22 Thread Qing Lv

Hi,


Gromos 54a7 force field has built-in topologies for some small molecules, like 
ATP. In these topologies, many atoms have names of up to 5 letters, such as 
AO1PA and AO2PB. However, PDB files seem do not support 5-letter atom names. 
So, if I name an atom "AO2PB" in PDB, it will be truncated to "AO2P" or "O2PB" 
when executing pdb2gmx, and these atoms cannot be recognized then.
Anyone know how to solvate this problem? Many thanks ^_^


Qing
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[gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults

2017-06-22 Thread Qing Lv

Dear All,


I am setting up a simulation of protein-ATP complex. I manually combined the 
coordinates and topologies of the protein and ATP together, and ran editconf 
and solvate successfully. However, when I ran grompp, errors occurred:
Syntax error - File forcefield.itp, line 4
Last line read:
'[ defaults ]'
Invalid order for directive defaults


I checked the .itp files I used and did not find "[ defaults ]" pattern. How to 
fix it?
Thanks,
Qing
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[gmx-users] g_rdf and g_select for number of res with COM within distance to surface

2017-06-22 Thread Patrick Charchar

Hi all,

I'm trying to calculate the number of residues (part of a residue) within a
distance (0.5 nm) to the surface of a molecule.

The molecule (MOL) is made up of 43 atoms.
The residues of interest are ASP (there's 36 of them in my system), but I'm
only interested in the COM between OD1 and OD2 (i.e. the two side chain
oxygens).

So essentially I want the distance between the COM of each OD1/OD2 pair in
reference to any atom of MOL.

To achieve this I have used g_select and g_rdf at a single frame but the
answers differ and I'm not sure why. I'm using version 4.6.5, but I've
tested this on 5.0.5 and the same result is observed.

The lines of interest are:
g_select -f ../trjs/*nj.xtc -s ../../vel1/md-tpr/*struct.tpr -n
../index.ndx -select 'res_com of group ASP_oxygens and within 0.5 of group
MOL' -oi closeASP.dat -resnr index -b 0 -e 0

echo 140 139 | g_rdf -f ../trjs/*nj.xtc -s ../../vel1/md-tpr/*struct.tpr -n
../index.ndx -o -cn -rdf res_com -surf mol -b 0 -e 0

(where group 140 is ASP_oxygens and group 139 is MOL)

The output from g_select -oi is:
0.000*7*   45   86  115  121  122  129  143

while from g_rdf -cn (at 0.5 nm) its:
0.5  *5*


So g_select says 7 residues are within 0.5 nm while g_rdf says 5 residues.

I've also tried at different frames, but always obtain different results
form the two tools and can't figure out why. Any insight would be
appreciated.

Cheers,
Patrick
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Re: [gmx-users] Constraint vs. Umbrella in Pull COM

2017-06-22 Thread Alex

In the case of SHAKE constraint, there is no spring-like physics, like in
umbrella pulling. The distance between COMs evolves according to the rate
you set, but there is no COM oscillation around prescribed values, SHAKE
turns the distance into a solid stick.

Alex

On Thu, Jun 22, 2017 at 5:13 PM, Angela Marcela Murcia Rios  wrote:

> Hi All,
>
>
> I was wondering if someone knows the difference between constraint versus
> umbrella pulling. I have read the manual but I'm still not sure what this
> means.
>
>
> 1. Umbrella pulling: A harmonic potential is applied between the centers
> of mass of two groups. Thus, the force is proportional to the displacement.
> 2. Constraint pulling: The distance between the centers of mass of two
> groups is constrained. The constraint force can be written to a file. This
> method uses the SHAKE algorithm but only needs 1 iteration to be exact if
> only two groups are constrained.
>
> What does it mean by "The distance between the centers of mass of two
> groups is constrained"? Is this distance fixed? or is the reference group
> assumed to be fixed?
>
> Thanks for the help!
>
> -Angela
>
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[gmx-users] Constraint vs. Umbrella in Pull COM

2017-06-22 Thread Angela Marcela Murcia Rios

Hi All,


I was wondering if someone knows the difference between constraint versus 
umbrella pulling. I have read the manual but I'm still not sure what this means.


1. Umbrella pulling: A harmonic potential is applied between the centers of 
mass of two groups. Thus, the force is proportional to the displacement.
2. Constraint pulling: The distance between the centers of mass of two groups 
is constrained. The constraint force can be written to a file. This method uses 
the SHAKE algorithm but only needs 1 iteration to be exact if only two groups 
are constrained.

What does it mean by "The distance between the centers of mass of two groups is 
constrained"? Is this distance fixed? or is the reference group assumed to be 
fixed?

Thanks for the help!

-Angela

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Re: [gmx-users] Computing work from pulling simulations

2017-06-22 Thread Lutz Maibaum

On Jun 21, 2017, at 2:32 AM, Leandro Bortot  wrote:
> 
> Have you compared the results of your calculation using the forces at
> different intervals? e.g. every 1, 10, 50, 100 steps ?
> 
> As long as you use a not-so-large interval the result should be the same
> within statistical error.

Yes, that is of course a possibility. I get about 2% relative error between 
writing out the forces at every timestep vs. writing them our only every 1000 
timesteps. That’s not the end of the world, but I was hoping to avoid it if 
Gromacs would keep track of the cumulative work performed by the umbrella 
potential.

Thanks for your reply!

Best,

Lutz

> On Mon, Jun 19, 2017 at 7:19 PM, Lutz Maibaum 
> wrote:
> 
>> I am using “umbrella pulling” to simulate the dissociation of two
>> molecules. I would like to calculate the work W(t) that the harmonic trap
>> has performed on my system up to timestep t, which can be calculated as
>> 
>> W(t) = sum_{i=0}^t F_i * v * dt
>> 
>> where F_i is the biasing force at timestep i, v is the pulling velocity,
>> and dt is the timestep. The latter two I set in the .mdp file, and the
>> force is written out by Gromacs to the  pull_pullf.xvg file.
>> 
>> This works very well. However, computing the work using the equation above
>> requires me to save the forces to a file _every single timestep_, which
>> becomes unfeasible for longer simulations. Does Gromacs keep track of the
>> cumulative work performed by the umbrella potential, and does it save that
>> value somewhere? I couldn’t find it in the .edr or log files (I am using
>> Gromacs 5.1.4).
>> 
>> Best,
>> 
>> Lutz

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Re: [gmx-users] System shrinkage during vacuum simulation

2017-06-22 Thread David van der Spoel


On 22/06/17 20:03, Sanim Rahman wrote:

Hello everyone,

I ran a short MD simulation with a 3dc ewald geometry to simulate a vacuum
slab at the top and bottom of my bilayer system. I equilibrated my system,
tripled the size of my system in the z-direction and then added the 3dc
geometry. My mdp script is written as below:


turn off p coupling

title = Production MD
; Run parameters
integrator = md
nsteps = 2500
dt= 0.002

; Output control
nstxout = 2000
nstvout = 2000
nstxtcout = 2000
nstenergy = 2000
nstlog = 2000

; Bond parameters
continuation = yes
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 1
lincs_order = 4

; Neighborsearching
ns_type = grid
nstlist = 5
rlist = 1.2
rcoulomb = 1.6
rvdw = 1.6

; Electrostatics
coulombtype = PME
pme_order = 4
fourierspacing = 0.16

; Temperature coupling is on
tcoupl = Nose-Hoover
tc-grps = System
tau_t = 0.2
ref_t = 310

; EWALD/PME/PPPM parameters =
ewald-geometry: 3dc

; Pressure coupling is on
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 2.0
ref_p = 1.0   1.0
compressibility = 4.5e-5 4.5e-5

; Periodic boundary conditions
pbc= xyz

; Dispersion correction
DispCorr = EnerPres

; Velocity generation
gen_vel = no

My system shrunk down to a value close to the original dimension in the z
direction as soon as the simulation started after I analyzed it using
g_energy. Is there a mistake with my production .mdp file?

I will truly appreciate your assistance.

Regards,
Sanim Rahman




--
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Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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[gmx-users] System shrinkage during vacuum simulation

2017-06-22 Thread Sanim Rahman

Hello everyone,

I ran a short MD simulation with a 3dc ewald geometry to simulate a vacuum
slab at the top and bottom of my bilayer system. I equilibrated my system,
tripled the size of my system in the z-direction and then added the 3dc
geometry. My mdp script is written as below:

title = Production MD
; Run parameters
integrator = md
nsteps = 2500
dt= 0.002

; Output control
nstxout = 2000
nstvout = 2000
nstxtcout = 2000
nstenergy = 2000
nstlog = 2000

; Bond parameters
continuation = yes
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 1
lincs_order = 4

; Neighborsearching
ns_type = grid
nstlist = 5
rlist = 1.2
rcoulomb = 1.6
rvdw = 1.6

; Electrostatics
coulombtype = PME
pme_order = 4
fourierspacing = 0.16

; Temperature coupling is on
tcoupl = Nose-Hoover
tc-grps = System
tau_t = 0.2
ref_t = 310

; EWALD/PME/PPPM parameters =
ewald-geometry: 3dc

; Pressure coupling is on
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 2.0
ref_p = 1.0   1.0
compressibility = 4.5e-5 4.5e-5

; Periodic boundary conditions
pbc= xyz

; Dispersion correction
DispCorr = EnerPres

; Velocity generation
gen_vel = no

My system shrunk down to a value close to the original dimension in the z
direction as soon as the simulation started after I analyzed it using
g_energy. Is there a mistake with my production .mdp file?

I will truly appreciate your assistance.

Regards,
Sanim Rahman
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Re: [gmx-users] Pulling inside a channel to calculate the PMF

2017-06-22 Thread Alex


I've never used PLUMED, to be honest, so I don't know.

If ligands are salt ions or any other overall charged entities, I would 
solvate the channel (with restraint, maybe) for essentially a production 
run and apply an electric field "parallel" to the channel lumen, then 
just visualize the trajectory and pick the configurations by hand. gmx 
trjconv can -dump any particular frame of your liking. Maybe not as 
automated as one could hope, but then you will know in-depth what 
configs you have.


Alex

On 6/22/2017 3:03 AM, François-Régis Chalaoux wrote:

Hi Alex,

There is no confusion about the pulling that is only a preparation for
WHAM, but as you tell it you need to choose positions. These positions
could be choosen manually: if one choose to explore the static channel from
apo, then I'm agree, select the positions in the channel "in a bunch of
reasonably spaced spots along the curved "axis" of your channel, each
followed by equilibration and the production run, yielding the data useful
for WHAM". As you say, you need time and patience. Could PLUMED (or
somethoing else) /Gromacs be used to automate this ?

On the other side, this channel come from a static APO structure and the
reality of this channel is tiedous, so why not discover dynamically the
channel and run the next equilibration and the production run on the fly, could
PLUMED (or somethoing else)/Gromacs  be used to automate this ? How to
discover the channel on the fly ? May be it is feasible to use simply the
coordinates of the channel discovered by MDPocket with a long classical MD
realized  previously on the apo/holo structure ?

FR.

2017-06-22 10:19 GMT+02:00 Alex :


I think your problem is solvable with enough perseverance, but there may
also be some confusion... The PMF calculation isn't based on the data
obtained from an actual pull: the pulling rate in those simulations is set
to zero. The reason for using pull code there is to pull (pun intended) the
positions and/or forces. The initial structures, of course, is where e.g.
Justin's tutorial uses pull along a straight line.

However, if you have the time and patience, you could of course
(manually?) put your ligand in a bunch of reasonably spaced spots along the
curved "axis" of your channel, each followed by equilibration and the
production run, yielding the data useful for WHAM.

Hope this helps.

Alex


On 6/22/2017 2:05 AM, François-Régis Chalaoux wrote:


Hi everybody,

I would like to pull a ligand in a channel from my protein and calculate
the PMF with Umbrella sampling. This channel is probably not linear and
thus have to be defined. Too much colisions appears along a simple one
axis
pulling and causing a catastrophic PMF calculation.

Currently I'm working with Gromacs and I wondered if it is possible to
define statically or dynamically the coordinates for the center of the
channel and use it during the simulation (Pulling).

One solution could be to define in the md_pull.mdp configuration file all
the transition points of my pathway through which my ligand must pass from
my APO structure determined with CAVER.
Instantiation of Gromacs parameters of md_pull.mdp is not enough clear for
me and PLUMED is may be a more direct solution. Currently I have no
experience with PLUMED but It seems on paper to be able.

An other choice would be to define dynamically the channel center,
on-the-fly. PLUMED seems also capable to manage this sort of challenge but
once again I have no idea of the feasibility of a such work.


What do you think about this problem and of the tracks evoked above ?


Cheers, FR.

*Pulling inside a channel to calculate the PMF*. Available from:
https://www.researchgate.net/post/Pulling_inside_a_channel_t
o_calculate_the_PMF#594b792648954cf7f2759a48
[accessed Jun 22, 2017].


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Re: [gmx-users] How to get the correct reference frame to run the rmsf?

2017-06-22 Thread Justin Lemkul




On 6/22/17 12:09 PM, ZHANG Cheng wrote:

Dear Gromacs,
I try to use this command to calculate RMSF:


echo 3 | gmx rmsf -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsf_20-30ns.xvg -oq 
bfac.pdb -res -b 2 -e 3


My simulation lasts for 30 ns, but I only want RMSF for the last 10 ns. It is mandatory 
to assign a reference frame, so I use "md_0_1.tpr", which gives the frame at 
time 0 ns.



The structure in -s is only used as a reference for fitting if you supply the 
-fit option, which you have not.  The only mandatory elements read from the .tpr 
are the masses and connectivity/residue information.  RMSF is always computed 
from the average structure in the analyzed time frame.




However, I think I should use a frame which is a time-averaged position within 
20-30 ns. Can I ask how to get this frame?



This is what the -ox option does.  It's not a reference frame, though, and the 
coordinates are going to be unphysical.




In addition, the command line outputs a PDB file. So what does this 
conformation represents, time 0, 20 or 30 ns?


Compare the coordinates with those snapshots and see :)

-Justin

--
==

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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

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[gmx-users] How to get the correct reference frame to run the rmsf?

2017-06-22 Thread ZHANG Cheng

Dear Gromacs,
I try to use this command to calculate RMSF:


echo 3 | gmx rmsf -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsf_20-30ns.xvg -oq 
bfac.pdb -res -b 2 -e 3


My simulation lasts for 30 ns, but I only want RMSF for the last 10 ns. It is 
mandatory to assign a reference frame, so I use "md_0_1.tpr", which gives the 
frame at time 0 ns.


However, I think I should use a frame which is a time-averaged position within 
20-30 ns. Can I ask how to get this frame?


In addition, the command line outputs a PDB file. So what does this 
conformation represents, time 0, 20 or 30 ns?


Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] Regarding the charge of the atom in the .rtp file

2017-06-22 Thread Justin Lemkul




On 6/22/17 11:23 AM, Dilip H N wrote:

No, its not related to parameterization methodology. it is a different
question...

how can i identify the molecule as methylamine (for example) since in the
.rtp the molecule type is written as [MAM1]
[ MAM1 ]
   [ atoms ]
N1 NG321-0.990  0
C1 CG3AM2 -0.060  1
   HN1 HGPAM20.390  2
   HN2 HGPAM20.390  3
   HC1 HGAAM20.090  4
   HC2 HGAAM20.090  5
   HC3 HGAAM20.090  6
   [ bonds ]
N1C1
N1   HN1
N1   HN2
C1   HC1
C1   HC2
C1   HC3
Is thr any hint such tht i can identify the molecule type written in .rtp
file.??
Or should i manually find it out..??... but in case of Glycine the molecule
type is [GLY] which is easy to find
How can i solve this issue..??



You need to go to the original CHARMM force field files.  These include names 
and (typically) chemical structure drawings.


http://mackerell.umaryland.edu/charmm_ff.shtml#charmm

-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] Regarding the charge of the atom in the .rtp file

2017-06-22 Thread Dilip H N

No, its not related to parameterization methodology. it is a different
question...

how can i identify the molecule as methylamine (for example) since in the
.rtp the molecule type is written as [MAM1]
[ MAM1 ]
  [ atoms ]
   N1 NG321-0.990  0
   C1 CG3AM2 -0.060  1
  HN1 HGPAM20.390  2
  HN2 HGPAM20.390  3
  HC1 HGAAM20.090  4
  HC2 HGAAM20.090  5
  HC3 HGAAM20.090  6
  [ bonds ]
   N1C1
   N1   HN1
   N1   HN2
   C1   HC1
   C1   HC2
   C1   HC3
Is thr any hint such tht i can identify the molecule type written in .rtp
file.??
Or should i manually find it out..??... but in case of Glycine the molecule
type is [GLY] which is easy to find
How can i solve this issue..??

Thank you...





   Sent with Mailtrack


On Thu, Jun 22, 2017 at 4:38 PM, Mark Abraham 
wrote:

> Hi,
>
> I don't understand what you are asking. How does it relate to
> parameterization methodology?
>
> Mark
>
> On Thu, Jun 22, 2017 at 7:20 AM Dilip H N 
> wrote:
>
> > Thank you for reply..
> >
> > But how can i identify the molecule as methylamine (for example) since in
> > the .rtp the molecule type is written as [MAM1]
> > [ MAM1 ]
> >   [ atoms ]
> >N1 NG321-0.990  0
> >C1 CG3AM2 -0.060  1
> >   HN1 HGPAM20.390  2
> >   HN2 HGPAM20.390  3
> >   HC1 HGAAM20.090  4
> >   HC2 HGAAM20.090  5
> >   HC3 HGAAM20.090  6
> >   [ bonds ]
> >N1C1
> >N1   HN1
> >N1   HN2
> >C1   HC1
> >C1   HC2
> >C1   HC3
> > Is thr any hint such tht i can identify the molecule type written in .rtp
> > file.??
> > Or should i manually find it out..??... but in case of Glycine the
> molecule
> > type is [GLY] which is easy to find
> > How can i solve this issue..??
> >
> > Thank you...
> >
> >
> >
> >    Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature=en;
> referral=cy16f01.di...@nitk.edu.in=22
> > >
> >
> > On Wed, Jun 21, 2017 at 4:23 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > On Wed, Jun 21, 2017 at 11:59 AM Dilip H N 
> > > wrote:
> > >
> > > > Hello all.
> > > > 1] I want to knw how the charges are designated/assigned for the each
> > > atoms
> > > > in molecule in the .rtp file.  ie., as example for methylamine in
> > CHARMM
> > > > FF:-
> > > >
> > > > [ MAM1 ]
> > > >   [ atoms ]
> > > >   N1 NG321-0.990  0
> > > >   C1 CG3AM2 -0.060  1
> > > >  HN1 HGPAM20.390  2
> > > >  HN2 HGPAM20.390  3
> > > >  HC1 HGAAM20.090  4
> > > >  HC2 HGAAM20.090  5
> > > >  HC3 HGAAM20.090  6
> > > >   [ bonds ]
> > > >   N1C1
> > > >   N1   HN1
> > > >   N1   HN2
> > > >   C1   HC1
> > > >   C1   HC2
> > > >   C1   HC3
> > > >  ie how are the charges -0.990, -0.060, 0.390 etc., are assigned...
> > > >
> > >
> > > The parameterization methodology is unique to each force field, and
> > perhaps
> > > to each tool that generates compatible topologies. You need to read
> that
> > > documentation and literature to understand how they were derived.
> > >
> > >
> > > > 2] and if i get the topology/itp file from the automated topology
> > builder
> > > > as in SwissParam for CHARMM forcefield, how can i confirm that the
> > > charges
> > > > assigned are exact..??
> > > >
> > >
> > > You can see if they are correct in the sense of being a valid model of
> > > reality by running a simulation and observing whether you can get
> > > reasonable agreement with suitable e.g. experimental data.
> > >
> > > Mark
> > >
> > >
> > > > Any help/suggestion is most welcome.
> > > > Thank you...
> > > > --
> > > > With Best Regards,
> > > >
> > > > DILIP.H.N
> > > > Ph.D Student
> > > >
> > > >
> > > >
> > > >    Sent with Mailtrack
> > > > <
> > > > https://mailtrack.io/install?source=signature=en;
> > > referral=cy16f01.di...@nitk.edu.in=22
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > With Best Regards,
>

Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

2017-06-22 Thread Mark Abraham

Hi,

On Thu, Jun 22, 2017 at 3:57 PM Diez Fernandez, Amanda <
amanda.die...@imperial.ac.uk> wrote:

> Hi Mark,
>
> Thanks.
>
> >mdrun will generally "make molecules whole" for -c, but otherwise doesn't
> >care. Implementing general triclininc 3D periodicity with domain
> >decomposition is a messy business.
>
> I am not using a triclinic unit cell (all angles are 90 in the input .pdb
> file). Wouldn¹t the output also be represented in a cuboid unit cell?
>

In this case, sure. I was merely illustrating why the code is complex and
doesn't necessarily work the way people assume.


> For this case ³making the molecule whole² is an arbitrary decision as it
> is an infinite substrate.
>

Sure, hence "generally"

Is this discrepancy something I should worry about, or is it just a
> question of visualisation?
>

There's no discrepancy. Which equivalent representation to use is arbitrary.

I am getting a warning  ³xx inconsistent shifts check your topology². I
> can¹t spot anything obvious and I do have periodic-molecules=yes in
> file.mdp.
>

I don't know what that means or how it should work. Very little testing of
that code takes place.

Mark


> Thanks!
> Amanda
>
>
>
>
>
>
>
> On 22/06/2017, 12:27, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se"
>  gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
>
> >Send gromacs.org_gmx-users mailing list submissions to
> >   gromacs.org_gmx-users@maillist.sys.kth.se
> >
> >To subscribe or unsubscribe via the World Wide Web, visit
> >   https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> >or, via email, send a message with subject or body 'help' to
> >   gromacs.org_gmx-users-requ...@maillist.sys.kth.se
> >
> >You can reach the person managing the list at
> >   gromacs.org_gmx-users-ow...@maillist.sys.kth.se
> >
> >When replying, please edit your Subject line so it is more specific
> >than "Re: Contents of gromacs.org_gmx-users digest..."
> >
> >
> >Today's Topics:
> >
> >   1. Re: Simulation of Carbon nanotube (Nikhil Maroli)
> >   2. Re: Regarding the charge of the atom in the .rtp file
> >  (Mark Abraham)
> >   3. Re: Difference between output_coordinates.gro and
> >  trajectory.xtc coordinates (Mark Abraham)
> >   4. Re: Difference between output_coordinates.gro and
> >  trajectory.xtc coordinates (Mark Abraham)
> >   5. Re: positive potential energy (Mark Abraham)
> >   6. Re: positive potential energy (Mark Abraham)
> >
> >
> >--
> >
> >Message: 1
> >Date: Thu, 22 Jun 2017 16:29:49 +0530
> >From: Nikhil Maroli 
> >To: gromacs.org_gmx-users@maillist.sys.kth.se
> >Subject: Re: [gmx-users] Simulation of Carbon nanotube
> >Message-ID:
> >   <
> camezy6syjjt2afora13b0oyp4316fwbxysx-j7nx36_6oup...@mail.gmail.com>
> >Content-Type: text/plain; charset="UTF-8"
> >
> >Dear Justin,
> >I have generated topology for CNT using gmx x2top. There is cyclic peptide
> >nanotube wrapped over the CNT (eight CP rings in equal intervals)
> >otherwise
> >let's say, CNT is inserted into the Cyclic peptide nanotube. I wanted to
> >put the whole system into the lipid bilayer. I was using charmm-gui for
> >the
> >input generator since it provides easy hand on CPN, So is it possible to
> >convert the CNT topology which generated with gmx x2top to 'Topology and
> >Parameters' for charmm-gui (*.rtf and *.prm)?
> >Thanks in advance.
> >
> >
> >--
> >
> >Message: 2
> >Date: Thu, 22 Jun 2017 11:08:45 +
> >From: Mark Abraham 
> >To: gmx-us...@gromacs.org
> >Subject: Re: [gmx-users] Regarding the charge of the atom in the .rtp
> >   file
> >Message-ID:
> >

Re: [gmx-users] Plotting Density Over Time?

2017-06-22 Thread Justin Lemkul




On 6/22/17 9:53 AM, Sanim Rahman wrote:

Hello everyone,

I am curious if there is a feature in g_density that will allow me to
calculate the density of my system at every single frame. I am hoping to
track density change over time to calculate membrane thickness (peak to
peak of electron density profile) and its standard deviation.



Use trjconv to dump out separate frames, then run gmx density in a loop over 
each in a simple shell script.


-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] Difference between output_coordinates.gro and trajectory.xtc coordinates

2017-06-22 Thread Diez Fernandez, Amanda

Hi Mark, 

Thanks.

>mdrun will generally "make molecules whole" for -c, but otherwise doesn't
>care. Implementing general triclininc 3D periodicity with domain
>decomposition is a messy business.
 
I am not using a triclinic unit cell (all angles are 90 in the input .pdb
file). Wouldn¹t the output also be represented in a cuboid unit cell?
For this case ³making the molecule whole² is an arbitrary decision as it
is an infinite substrate.
Is this discrepancy something I should worry about, or is it just a
question of visualisation?
 
I am getting a warning  ³xx inconsistent shifts check your topology². I
can¹t spot anything obvious and I do have periodic-molecules=yes in
file.mdp. 

Thanks!
Amanda
 






On 22/06/2017, 12:27, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se"
 wrote:

>Send gromacs.org_gmx-users mailing list submissions to
>   gromacs.org_gmx-users@maillist.sys.kth.se
>
>To subscribe or unsubscribe via the World Wide Web, visit
>   https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>or, via email, send a message with subject or body 'help' to
>   gromacs.org_gmx-users-requ...@maillist.sys.kth.se
>
>You can reach the person managing the list at
>   gromacs.org_gmx-users-ow...@maillist.sys.kth.se
>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
>Today's Topics:
>
>   1. Re: Simulation of Carbon nanotube (Nikhil Maroli)
>   2. Re: Regarding the charge of the atom in the .rtp file
>  (Mark Abraham)
>   3. Re: Difference between output_coordinates.gro and
>  trajectory.xtc coordinates (Mark Abraham)
>   4. Re: Difference between output_coordinates.gro and
>  trajectory.xtc coordinates (Mark Abraham)
>   5. Re: positive potential energy (Mark Abraham)
>   6. Re: positive potential energy (Mark Abraham)
>
>
>--
>
>Message: 1
>Date: Thu, 22 Jun 2017 16:29:49 +0530
>From: Nikhil Maroli 
>To: gromacs.org_gmx-users@maillist.sys.kth.se
>Subject: Re: [gmx-users] Simulation of Carbon nanotube
>Message-ID:
>   
>Content-Type: text/plain; charset="UTF-8"
>
>Dear Justin,
>I have generated topology for CNT using gmx x2top. There is cyclic peptide
>nanotube wrapped over the CNT (eight CP rings in equal intervals)
>otherwise
>let's say, CNT is inserted into the Cyclic peptide nanotube. I wanted to
>put the whole system into the lipid bilayer. I was using charmm-gui for
>the
>input generator since it provides easy hand on CPN, So is it possible to
>convert the CNT topology which generated with gmx x2top to 'Topology and
>Parameters' for charmm-gui (*.rtf and *.prm)?
>Thanks in advance.
>
>
>--
>
>Message: 2
>Date: Thu, 22 Jun 2017 11:08:45 +
>From: Mark Abraham 
>To: gmx-us...@gromacs.org
>Subject: Re: [gmx-users] Regarding the charge of the atom in the .rtp
>   file
>Message-ID:
>

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

2017-06-22 Thread gozde ergin

Thank Justin.
Mark you are right. I did not think about to check the manual. 

Thanks again.
> On 22 Jun 2017, at 15:51, Mark Abraham  wrote:
> 
> Hi,
> 
> I'd start by looking in the documentation. Section 5.3.2 of the manual
> clearly suggests putting it in the ffnonbonded.itp file, which is where you
> expected to find it at the start of this thread, right? :-)
> 
> Mark
> 
> On Thu, Jun 22, 2017 at 3:47 PM gozde ergin  > wrote:
> 
>> Hey Justin,
>> 
>> I figured out how they calculated the sigma values.
>> Basically they just take the geometric mean of nitrogen and oxygen sigma
>> and epsilon from ffnonbed.itp file in OPLS-AA force field
>> and calculated the pairwise LJ for N-O interaction.
>> 
>> Now I also try to add this information in my topol.top file.
>> In order to do that as you have mentioned I added a section ,
>> 
>> [ nonbond_params ]
>> ; i j   funcsigma   epsilon
>> opls_287  opls_272  1  0.323161248385416  0.790543521382599
>> 
>> 
>> after [ atoms ] section however I am facing with an error :
>> 
>> Fatal error:
>> Syntax error - File topol.top, line 42
>> Last line read:
>> '[ nonbond_params ]'
>> Invalid order for directive nonbond_params
>> 
>> Any suggestion would be appreciated.
>> 
>>> On 21 Jun 2017, at 16:46, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
>>> On 6/21/17 10:39 AM, gozde ergin wrote:
 Hi MArk,
 Thanks for the respond. I understood that point however I still do not
>> get which sigma to change.
 I the paper JCTC 2017, Miller et. al. they have mentioned that they
>> increase the for nitrogen–carboxylate oxygen interactions in OPLSAA.
 However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino
>> notrogen and one for carboxylate oxygen.
 
>>   sigmaepsilon
 opls_287   N3   7  14.00670-0.300   A3.25000e-01
>> 7.11280e-01
 opls_272   O2   8  15.99940-0.800   A2.96000e-01
>> 8.78640e-01
 Which one defines the amino nitrogen–carboxylate oxygen interactions?
 Which sigma should I change?
>>> 
>>> What people are doing more and more is introducing pair-specific
>> parameters to override the combination rule values.  That's likely what is
>> being referred to. OPLS-AA by default does not use pair-specific LJ
>> interactions, hence why you find no [nonbond_params] in ffnonbonded.itp.
>> The same is true of AMBER.  CHARMM uses some (also called NBFIX in the
>> literature), while GROMOS uses a ton of these.
>>> 
>>> To override the LJ combination rules, add a [nonbond_params] directive
>> with the published parameters, which refer to an *interaction*, not an atom
>> type.
>>> 
>>> -Justin
>>> 
 Thanks
> On 21 Jun 2017, at 16:21, Mark Abraham 
>> wrote:
> 
> Hi,
> 
> Different force fields work differently and thus are implemented
> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that
>> sigma
> is a property of the atomtype
> 
> Mark
> 
> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin 
>> wrote:
> 
>> Dear users,
>> 
>> I am trying to change the sigma value of amino nitrogen–carboxylate
>> oxygen
>> interactions in OPLSAA in GROMACS.
>> However I have difficulties to understand which parameter i should
>> change
>> in ffnonbonded.itp file?
>> I am looking something like [ nonbond_params ] section however it is
>> not
>> exist in ffnonbonded.itp?
>> Any help would be appreciated.
>> 
>> Thanks in advance.
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
> 
> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>> 
>>> --
>>> ==
>>> 
>>> 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 
>>>  > jalem...@outerbanks.umaryland.edu 
>>

[gmx-users] Plotting Density Over Time?

2017-06-22 Thread Sanim Rahman

Hello everyone,

I am curious if there is a feature in g_density that will allow me to
calculate the density of my system at every single frame. I am hoping to
track density change over time to calculate membrane thickness (peak to
peak of electron density profile) and its standard deviation.

Regards,
Sanim Rahman
-- 
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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Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

2017-06-22 Thread Mark Abraham

Hi,

I'd start by looking in the documentation. Section 5.3.2 of the manual
clearly suggests putting it in the ffnonbonded.itp file, which is where you
expected to find it at the start of this thread, right? :-)

Mark

On Thu, Jun 22, 2017 at 3:47 PM gozde ergin  wrote:

> Hey Justin,
>
> I figured out how they calculated the sigma values.
> Basically they just take the geometric mean of nitrogen and oxygen sigma
> and epsilon from ffnonbed.itp file in OPLS-AA force field
> and calculated the pairwise LJ for N-O interaction.
>
> Now I also try to add this information in my topol.top file.
> In order to do that as you have mentioned I added a section ,
>
> [ nonbond_params ]
> ; i j   funcsigma   epsilon
> opls_287  opls_272  1  0.323161248385416  0.790543521382599
>
>
> after [ atoms ] section however I am facing with an error :
>
> Fatal error:
> Syntax error - File topol.top, line 42
> Last line read:
> '[ nonbond_params ]'
> Invalid order for directive nonbond_params
>
> Any suggestion would be appreciated.
>
> > On 21 Jun 2017, at 16:46, Justin Lemkul  wrote:
> >
> >
> >
> > On 6/21/17 10:39 AM, gozde ergin wrote:
> >> Hi MArk,
> >> Thanks for the respond. I understood that point however I still do not
> get which sigma to change.
> >> I the paper JCTC 2017, Miller et. al. they have mentioned that they
> increase the for nitrogen–carboxylate oxygen interactions in OPLSAA.
> >> However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino
> notrogen and one for carboxylate oxygen.
> >>
>sigmaepsilon
> >>  opls_287   N3   7  14.00670-0.300   A3.25000e-01
> 7.11280e-01
> >>  opls_272   O2   8  15.99940-0.800   A2.96000e-01
> 8.78640e-01
> >> Which one defines the amino nitrogen–carboxylate oxygen interactions?
> >> Which sigma should I change?
> >
> > What people are doing more and more is introducing pair-specific
> parameters to override the combination rule values.  That's likely what is
> being referred to. OPLS-AA by default does not use pair-specific LJ
> interactions, hence why you find no [nonbond_params] in ffnonbonded.itp.
> The same is true of AMBER.  CHARMM uses some (also called NBFIX in the
> literature), while GROMOS uses a ton of these.
> >
> > To override the LJ combination rules, add a [nonbond_params] directive
> with the published parameters, which refer to an *interaction*, not an atom
> type.
> >
> > -Justin
> >
> >> Thanks
> >>> On 21 Jun 2017, at 16:21, Mark Abraham 
> wrote:
> >>>
> >>> Hi,
> >>>
> >>> Different force fields work differently and thus are implemented
> >>> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that
> sigma
> >>> is a property of the atomtype
> >>>
> >>> Mark
> >>>
> >>> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin 
> wrote:
> >>>
>  Dear users,
> 
>  I am trying to change the sigma value of amino nitrogen–carboxylate
> oxygen
>  interactions in OPLSAA in GROMACS.
>  However I have difficulties to understand which parameter i should
> change
>  in ffnonbonded.itp file?
>  I am looking something like [ nonbond_params ] section however it is
> not
>  exist in ffnonbonded.itp?
>  Any help would be appreciated.
> 
>  Thanks in advance.
>  --
>  Gromacs Users mailing list
> 
>  * Please search the archive at
>  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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> >
> > --
> > ==
> >
> > 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  jalem...@outerbanks.umaryland.edu> | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul <
> http://mackerell.umaryland.edu/~jalemkul>
> >
> > ==
> > --
> > Gromacs Users mailing list
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> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List <
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>

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

2017-06-22 Thread Justin Lemkul




On 6/22/17 9:47 AM, gozde ergin wrote:

Hey Justin,

I figured out how they calculated the sigma values.
Basically they just take the geometric mean of nitrogen and oxygen sigma and 
epsilon from ffnonbed.itp file in OPLS-AA force field
and calculated the pairwise LJ for N-O interaction.

Now I also try to add this information in my topol.top file.
In order to do that as you have mentioned I added a section ,

[ nonbond_params ]
; i j   funcsigma   epsilon
opls_287  opls_272  1  0.323161248385416  0.790543521382599


after [ atoms ] section however I am facing with an error :

Fatal error:
Syntax error - File topol.top, line 42
Last line read:
'[ nonbond_params ]'
Invalid order for directive nonbond_params

Any suggestion would be appreciated.



You can't declare force field parameters after you've introduced a 
[moleculetype].  Put it in ffnonbonded.itp or immediately after the #include 
statement for the force field.


-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] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

2017-06-22 Thread gozde ergin

Hey Justin,

I figured out how they calculated the sigma values. 
Basically they just take the geometric mean of nitrogen and oxygen sigma and 
epsilon from ffnonbed.itp file in OPLS-AA force field 
and calculated the pairwise LJ for N-O interaction.

Now I also try to add this information in my topol.top file. 
In order to do that as you have mentioned I added a section ,

[ nonbond_params ]
; i j   funcsigma   epsilon
opls_287  opls_272  1  0.323161248385416  0.790543521382599


after [ atoms ] section however I am facing with an error :

Fatal error:
Syntax error - File topol.top, line 42
Last line read:
'[ nonbond_params ]'
Invalid order for directive nonbond_params

Any suggestion would be appreciated.

> On 21 Jun 2017, at 16:46, Justin Lemkul  wrote:
> 
> 
> 
> On 6/21/17 10:39 AM, gozde ergin wrote:
>> Hi MArk,
>> Thanks for the respond. I understood that point however I still do not get 
>> which sigma to change.
>> I the paper JCTC 2017, Miller et. al. they have mentioned that they increase 
>> the for nitrogen–carboxylate oxygen interactions in OPLSAA.
>> However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino 
>> notrogen and one for carboxylate oxygen.
>>  
>>  sigmaepsilon
>>  opls_287   N3   7  14.00670-0.300   A3.25000e-01  7.11280e-01
>>  opls_272   O2   8  15.99940-0.800   A2.96000e-01  8.78640e-01
>> Which one defines the amino nitrogen–carboxylate oxygen interactions?
>> Which sigma should I change?
> 
> What people are doing more and more is introducing pair-specific parameters 
> to override the combination rule values.  That's likely what is being 
> referred to. OPLS-AA by default does not use pair-specific LJ interactions, 
> hence why you find no [nonbond_params] in ffnonbonded.itp.  The same is true 
> of AMBER.  CHARMM uses some (also called NBFIX in the literature), while 
> GROMOS uses a ton of these.
> 
> To override the LJ combination rules, add a [nonbond_params] directive with 
> the published parameters, which refer to an *interaction*, not an atom type.
> 
> -Justin
> 
>> Thanks
>>> On 21 Jun 2017, at 16:21, Mark Abraham  wrote:
>>> 
>>> Hi,
>>> 
>>> Different force fields work differently and thus are implemented
>>> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma
>>> is a property of the atomtype
>>> 
>>> Mark
>>> 
>>> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin  wrote:
>>> 
 Dear users,
 
 I am trying to change the sigma value of amino nitrogen–carboxylate oxygen
 interactions in OPLSAA in GROMACS.
 However I have difficulties to understand which parameter i should change
 in ffnonbonded.itp file?
 I am looking something like [ nonbond_params ] section however it is not
 exist in ffnonbonded.itp?
 Any help would be appreciated.
 
 Thanks in advance.
 --
 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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 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.
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> 
> -- 
> ==
> 
> 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] Domain decomposition

2017-06-22 Thread Sergio Manzetti

Thanks! I reduced the number to 4, and it works: 

gmx mdrun -v -dds 0.37 -nt 4 

Cheers 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Thursday, June 22, 2017 3:28:32 PM 
Subject: Re: [gmx-users] Domain decomposition 

On 6/22/17 9:22 AM, Sergio Manzetti wrote: 
> Checked the link, nothing written here on rcon and dds... 
> 

"Thus it is not possible to run a small simulation with large numbers of 
processors." 

Google will help you find more suggestions. 

-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] Domain decomposition

2017-06-22 Thread Justin Lemkul




On 6/22/17 9:22 AM, Sergio Manzetti wrote:

Checked the link, nothing written here on rcon and dds...



"Thus it is not possible to run a small simulation with large numbers of 
processors."


Google will help you find more suggestions.

-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] MDP for DNA with ions

2017-06-22 Thread Justin Lemkul




On 6/22/17 9:21 AM, Sergio Manzetti wrote:

Justin, I fixed the sim.mdp, however I realized I sent you the wrong mdp file, 
the one that gave DNA minimization problem is the EM.mdp

Which is this:

define =
integrator = steep
emtol = 100.0
emstep = 0.001
nsteps = 10
; output frequency
nstxout = 50
nstvout = 0
nstfout = 0
nstlog = 50
nstenergy = 50
nstxtcout = 0
xtc_grps = system
;
nstlist = 10
pbc = xyz
rlist = 0.8
cutoff-scheme = group
coulombtype = PME
rcoulomb = 0.8
vdwtype = cut-off
rvdw = 0.8
DispCorr = EnerPres
;
constraints = none
constraint_algorithm = LINCS
implicit_solvent = no
E_x =
E_y =
E_z =


However, it looks completely normal...


Still the system is not apprently equilibrated

1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out 
of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



Follow the link I provided before about diagnosing the problem.

-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] Domain decomposition

2017-06-22 Thread Sergio Manzetti

Checked the link, nothing written here on rcon and dds... 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Thursday, June 22, 2017 3:21:28 PM 
Subject: Re: [gmx-users] Domain decomposition 

On 6/22/17 9:16 AM, Sergio Manzetti wrote: 
> Hi, I have (also) a system of one molecule in water box of 3 3 3 dimensions, 
> the procedure goes well all the way till the simulation starts, getting: 
> 
> Will use 20 particle-particle and 4 PME only ranks 
> This is a guess, check the performance at the end of the log file 
> 
> --- 
> Program gmx mdrun, VERSION 5.1.2 
> Source code file: 
> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/domdec/domdec.cpp, line: 6987 
> 
> Fatal error: 
> There is no domain decomposition for 20 ranks that is compatible with the 
> given box and a minimum cell size of 2.0777 nm 
> Change the number of ranks or mdrun option -rcon or -dds or your LINCS 
> settings 
> Look in the log file for details on the domain decomposition 
> For more information and tips for troubleshooting, please check the GROMACS 
> website at http://www.gromacs.org/Documentation/Errors 
> --- 
> 
> 
> Not sure what to do here.. 
> 

Follow the link provided in the error message. 

-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] MDP for DNA with ions

2017-06-22 Thread Sergio Manzetti

Justin, I fixed the sim.mdp, however I realized I sent you the wrong mdp file, 
the one that gave DNA minimization problem is the EM.mdp 

Which is this: 

define = 
integrator = steep 
emtol = 100.0 
emstep = 0.001 
nsteps = 10 
; output frequency 
nstxout = 50 
nstvout = 0 
nstfout = 0 
nstlog = 50 
nstenergy = 50 
nstxtcout = 0 
xtc_grps = system 
; 
nstlist = 10 
pbc = xyz 
rlist = 0.8 
cutoff-scheme = group 
coulombtype = PME 
rcoulomb = 0.8 
vdwtype = cut-off 
rvdw = 0.8 
DispCorr = EnerPres 
; 
constraints = none 
constraint_algorithm = LINCS 
implicit_solvent = no 
E_x = 
E_y = 
E_z = 

However, it looks completely normal... 

Still the system is not apprently equilibrated 

1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out 
of the domain decomposition cell of their charge group in dimension x. 
This usually means that your system is not well equilibrated. 
For more information and tips for troubleshooting, please check the GROMACS 
website at http://www.gromacs.org/Documentation/Errors 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Thursday, June 22, 2017 3:17:02 PM 
Subject: Re: [gmx-users] MDP for DNA with ions 

On 6/22/17 9:09 AM, Sergio Manzetti wrote: 
> I use the AMBER99SB-ILDN ff for a piece of DNA taken from the RCSB database. 
> Removed all waters and non-nucleic acid molecules, and everything seems fine. 
> 
> The mdp settings are: 
> 
> title = DNA in water stabilization 
> cpp = /lib/cpp 
> include = -I../top 
> define = 
> integrator = md 
> dt = 0.002 
> nsteps = 500 
> nstxout = 5000 
> nstvout = 5000 
> nstlog = 5000 
> nstenergy = 300 
> nstxout-compressed = 300 
> compressed-x-grps = DNA SOL NA CL 
> energygrps = DNA SOL NA CL 
> nstlist = 10 
> ns-type = grid 
> rlist = 1.2 
> coulombtype = PME 
> rcoulomb = 1.2 
> rvdw = 1.2 

AMBER uses shorter cutoffs. Refer to their papers for what is correct. 

> tcoupl = V-Rescale 
> tc-grps = DNA SOL NA CL 
> tau-t = 0.1 0.1 0.1 0.1 
> ref-t = 310 310 310 310 

Don't do this. 

http://www.gromacs.org/Documentation/Terminology/Thermostats#What_No_To_Do 

> Pcoupl = No 
> tau-p = 1.0 
> compressibility = 4.5e-5 
> ref-p = 1.0 
> gen-vel = yes 
> gen-temp = 310 
> gen-seed = 173529 
> constraints = all-bonds 

IIRC AMBER only constrains bonds to H, so again check the literature. 

None of these points is likely fatal (maybe the thermostat) but you should use 
correct settings. If your system is crashing with this .mdp file or the 
corrected one, it's because you haven't adequately minimized and equilibrated. 

-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] Domain decomposition

2017-06-22 Thread Justin Lemkul




On 6/22/17 9:16 AM, Sergio Manzetti wrote:

Hi, I have (also) a system of one molecule in water box of 3 3 3 dimensions, 
the procedure goes well all the way till the simulation starts, getting:

Will use 20 particle-particle and 4 PME only ranks
This is a guess, check the performance at the end of the log file

---
Program gmx mdrun, VERSION 5.1.2
Source code file: 
/build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/domdec/domdec.cpp, line: 6987

Fatal error:
There is no domain decomposition for 20 ranks that is compatible with the given 
box and a minimum cell size of 2.0777 nm
Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


Not sure what to do here..



Follow the link provided in the error message.

-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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[gmx-users] Domain decomposition

2017-06-22 Thread Sergio Manzetti

Hi, I have (also) a system of one molecule in water box of 3 3 3 dimensions, 
the procedure goes well all the way till the simulation starts, getting: 

Will use 20 particle-particle and 4 PME only ranks 
This is a guess, check the performance at the end of the log file 

--- 
Program gmx mdrun, VERSION 5.1.2 
Source code file: 
/build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/domdec/domdec.cpp, line: 6987 

Fatal error: 
There is no domain decomposition for 20 ranks that is compatible with the given 
box and a minimum cell size of 2.0777 nm 
Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings 
Look in the log file for details on the domain decomposition 
For more information and tips for troubleshooting, please check the GROMACS 
website at http://www.gromacs.org/Documentation/Errors 
--- 


Not sure what to do here.. 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
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Tlf: +47 57695621 
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Re: [gmx-users] MDP for DNA with ions

2017-06-22 Thread Sergio Manzetti

OK, thanks for this! 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Thursday, June 22, 2017 3:17:02 PM 
Subject: Re: [gmx-users] MDP for DNA with ions 

On 6/22/17 9:09 AM, Sergio Manzetti wrote: 
> I use the AMBER99SB-ILDN ff for a piece of DNA taken from the RCSB database. 
> Removed all waters and non-nucleic acid molecules, and everything seems fine. 
> 
> The mdp settings are: 
> 
> title = DNA in water stabilization 
> cpp = /lib/cpp 
> include = -I../top 
> define = 
> integrator = md 
> dt = 0.002 
> nsteps = 500 
> nstxout = 5000 
> nstvout = 5000 
> nstlog = 5000 
> nstenergy = 300 
> nstxout-compressed = 300 
> compressed-x-grps = DNA SOL NA CL 
> energygrps = DNA SOL NA CL 
> nstlist = 10 
> ns-type = grid 
> rlist = 1.2 
> coulombtype = PME 
> rcoulomb = 1.2 
> rvdw = 1.2 

AMBER uses shorter cutoffs. Refer to their papers for what is correct. 

> tcoupl = V-Rescale 
> tc-grps = DNA SOL NA CL 
> tau-t = 0.1 0.1 0.1 0.1 
> ref-t = 310 310 310 310 

Don't do this. 

http://www.gromacs.org/Documentation/Terminology/Thermostats#What_No_To_Do 

> Pcoupl = No 
> tau-p = 1.0 
> compressibility = 4.5e-5 
> ref-p = 1.0 
> gen-vel = yes 
> gen-temp = 310 
> gen-seed = 173529 
> constraints = all-bonds 

IIRC AMBER only constrains bonds to H, so again check the literature. 

None of these points is likely fatal (maybe the thermostat) but you should use 
correct settings. If your system is crashing with this .mdp file or the 
corrected one, it's because you haven't adequately minimized and equilibrated. 

-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 
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Re: [gmx-users] MDP for DNA with ions

2017-06-22 Thread Justin Lemkul




On 6/22/17 9:09 AM, Sergio Manzetti wrote:

I use the AMBER99SB-ILDN ff for a piece of DNA taken from the RCSB database. 
Removed all waters and non-nucleic acid molecules, and everything seems fine.

The mdp settings are:

title = DNA in water stabilization
cpp = /lib/cpp
include = -I../top
define =
integrator = md
dt = 0.002
nsteps = 500
nstxout = 5000
nstvout = 5000
nstlog = 5000
nstenergy = 300
nstxout-compressed = 300
compressed-x-grps = DNA SOL NA CL
energygrps = DNA SOL NA CL
nstlist = 10
ns-type = grid
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.2


AMBER uses shorter cutoffs.  Refer to their papers for what is correct.


tcoupl = V-Rescale
tc-grps = DNA SOL NA CL
tau-t = 0.1 0.1 0.1 0.1
ref-t = 310 310 310 310


Don't do this.

http://www.gromacs.org/Documentation/Terminology/Thermostats#What_No_To_Do


Pcoupl = No
tau-p = 1.0
compressibility = 4.5e-5
ref-p = 1.0
gen-vel = yes
gen-temp = 310
gen-seed = 173529
constraints = all-bonds


IIRC AMBER only constrains bonds to H, so again check the literature.

None of these points is likely fatal (maybe the thermostat) but you should use 
correct settings.  If your system is crashing with this .mdp file or the 
corrected one, it's because you haven't adequately minimized and equilibrated.


-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] MDP for DNA with ions

2017-06-22 Thread Sergio Manzetti

I use the AMBER99SB-ILDN ff for a piece of DNA taken from the RCSB database. 
Removed all waters and non-nucleic acid molecules, and everything seems fine. 

The mdp settings are: 

title = DNA in water stabilization 
cpp = /lib/cpp 
include = -I../top 
define = 
integrator = md 
dt = 0.002 
nsteps = 500 
nstxout = 5000 
nstvout = 5000 
nstlog = 5000 
nstenergy = 300 
nstxout-compressed = 300 
compressed-x-grps = DNA SOL NA CL 
energygrps = DNA SOL NA CL 
nstlist = 10 
ns-type = grid 
rlist = 1.2 
coulombtype = PME 
rcoulomb = 1.2 
rvdw = 1.2 
tcoupl = V-Rescale 
tc-grps = DNA SOL NA CL 
tau-t = 0.1 0.1 0.1 0.1 
ref-t = 310 310 310 310 
Pcoupl = No 
tau-p = 1.0 
compressibility = 4.5e-5 
ref-p = 1.0 
gen-vel = yes 
gen-temp = 310 
gen-seed = 173529 
constraints = all-bonds 

Sergio 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Thursday, June 22, 2017 3:07:03 PM 
Subject: Re: [gmx-users] MDP for DNA with ions 

On 6/22/17 8:56 AM, Sergio Manzetti wrote: 
> HI, I use mdp for simulating with a 2fs time step, nstlist 10, rlist 1.2, 
> rcoulomb 1.2, rvdw 1.2, V-rescale, no P-coupling. Lincs on all bonds, still 
> the DNA system won't minimize . 
> 
> What is your experience with DNA simulations and these settings? Do you have 
> an mdp file that may be generally good for DNA sims? 
> 

Settings depend on the force field, not the molecules in the system. If you 
want commentary, please provide a full .mdp file, not just select settings. 

-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] MDP for DNA with ions

2017-06-22 Thread Justin Lemkul




On 6/22/17 8:56 AM, Sergio Manzetti wrote:

HI, I use mdp for simulating with a 2fs time step, nstlist 10, rlist 1.2, 
rcoulomb 1.2, rvdw 1.2, V-rescale, no P-coupling. Lincs on all bonds, still the 
DNA system won't minimize .

What is your experience with DNA simulations and these settings? Do you have an 
mdp file that may be generally good for DNA sims?



Settings depend on the force field, not the molecules in the system.  If you 
want commentary, please provide a full .mdp file, not just select settings.


-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] Genion

2017-06-22 Thread Sergio Manzetti

Indeed. Thanks! 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Mark Abraham"  
To: "gmx-users"  
Sent: Thursday, June 22, 2017 2:29:54 PM 
Subject: Re: [gmx-users] Genion 

Hi, 

The error message has a helpful URL that'll take you to the same advice 
that we give several times a week on here :-) 

Mark 

On Thu, 22 Jun 2017 14:27 Sergio Manzetti  
wrote: 

> Thanks, Worked out. Now I got a note saying: 
> 
> NOTE 1 [file em.mdp]: 
> The group cutoff scheme is deprecated since GROMACS 5.0 and will be 
> removed in a future release when all interaction forms are supported for 
> the verlet scheme. The verlet scheme already scales better, and it is 
> compatible with GPUs and other accelerators. 
> 
> 
> 
> Fatal error: 
> 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off 
> out of the domain decomposition cell of their charge group in dimension x. 
> This usually means that your system is not well equilibrated. 
> For more information and tips for troubleshooting, please check the GROMACS 
> website at http://www.gromacs.org/Documentation/Errors 
> 
> 
> 
> How can I fix the system, when the energy minimization step cannot? 
> 
> 
> Sergio 
> 
> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ 
> | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ 
> http://www.phap.no/ | FAP ] 
> 
> 
> 
> From: "Justin Lemkul"  
> To: "gmx-users"  
> Sent: Thursday, June 22, 2017 2:21:17 PM 
> Subject: Re: [gmx-users] Genion 
> 
> On 6/22/17 8:14 AM, Sergio Manzetti wrote: 
> > OK, now I treied writing Na Cl and not NA and CL and get: 
> > 
> 
> This is what you did before, so naturally you get the same thing. 
> 
> > Na) 
> > Warning: atom name 11966 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> > Warning: atom name 11967 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> > Warning: atom name 11968 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> > Warning: atom name 11969 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> > Warning: atom name 11970 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> > 
> 
> As I said, using mixed case is incorrect. The [moleculetype] entries in 
> ions.itp expect all caps. Use all caps. 
> 
> -Justin 
> 
> > 
> > 
> > 
> > 
> > Sergio Manzetti 
> > 
> > [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> > 
> > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ 
> http://www.fjordforsk.no/ | ] 
> > Midtun 
> > 6894 Vangsnes 
> > Norge 
> > Org.nr. 911 659 654 
> > Tlf: +47 57695621 
> > [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ 
> | FAP ] 
> > 
> > 
> > 
> > From: "Justin Lemkul"  
> > To: "gmx-users"  
> > Sent: Thursday, June 22, 2017 2:09:02 PM 
> > Subject: Re: [gmx-users] Genion 
> > 
> > On 6/22/17 7:30 AM, Sergio Manzetti wrote: 
> >> Hi, the procedure as defined by Juistin worked out well. However, a new 
> problem has occurred. At mdrun for the minimization, I get: 
> >> 
> >> --- 
> >> Program gmx mdrun, VERSION 5.1.2 
> >> Source code file: 
> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/ewald/pme-redistribute.cpp, 
> line: 276 
> >> 
> >> Fatal error: 
> >> 1 particles communicated to PME rank 3 are more than 2/3 times the 
> cut-off out of the domain decomposition cell of their charge group in 
> dimension x. 
> >> This usually means that your system is not well equilibrated. 
> >> For more information and tips for troubleshooting, please check the 
> GROMACS 
> >> website at http://www.gromacs.org/Documentation/Errors 
> >> 
> >> 
> >> This may be caused by the solvent replacement of genion by Na Cl: 
> >> 
> >> 
> >> 
> >> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision) 
> >> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision) 
> >> Will try to add 130 Na ions and 90 Cl ions. 
> >> Select a continuous group of solvent molecules 
> >> Group 0 ( System) has 98254 elements 
> >> Group 1 ( DNA) has 1333 elements 
> >> Group 2 ( Water) has 96921 elements 
> >> Group 3 ( SOL) has 96921 elements 
> >> Group 4 ( non-Water) has 1333 elements 
> >> Select a group: 3 
> >>

Re: [gmx-users] Simulation of Carbon nanotube

2017-06-22 Thread Justin Lemkul




On 6/22/17 8:31 AM, Nikhil Maroli wrote:

Thanks,
I have given the image of the system in the below link.

I thought if I can get Topology and Parameters for CNT alone would be
better to go with Charmm-gui. Since I can treat CNT as ligand and upload
the parameters will work with the server so in this aspects any suggestion?
like how to get those parameters for CNT? Sorry, it is somewhat out of
GROMACS question.

https://drive.google.com/file/d/0BxaQk_pcR9vicWdDdWV1T0YwTUE/view?usp=sharing



I understand what you're doing, I'm just not sure it's worth the effort to try 
to convert topology and parameter information to CHARMM format (especially if 
you're not familiar with it) for a periodic molecule (which I honestly don't 
know if CHARMM will handle correctly).


-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] Simulation of Carbon nanotube

2017-06-22 Thread Nikhil Maroli

Thanks,
I have given the image of the system in the below link.

I thought if I can get Topology and Parameters for CNT alone would be
better to go with Charmm-gui. Since I can treat CNT as ligand and upload
the parameters will work with the server so in this aspects any suggestion?
like how to get those parameters for CNT? Sorry, it is somewhat out of
GROMACS question.

https://drive.google.com/file/d/0BxaQk_pcR9vicWdDdWV1T0YwTUE/view?usp=sharing

Thanks in advance.
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Re: [gmx-users] Genion

2017-06-22 Thread Sergio Manzetti

THanks Justin. 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Thursday, June 22, 2017 2:29:40 PM 
Subject: Re: [gmx-users] Genion 

On 6/22/17 8:22 AM, Sergio Manzetti wrote: 
> Thanks, Worked out. Now I got a note saying: 
> 
> NOTE 1 [file em.mdp]: 
> The group cutoff scheme is deprecated since GROMACS 5.0 and will be 
> removed in a future release when all interaction forms are supported for 
> the verlet scheme. The verlet scheme already scales better, and it is 
> compatible with GPUs and other accelerators. 
> 
> 
> 
> Fatal error: 
> 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off 
> out of the domain decomposition cell of their charge group in dimension x. 
> This usually means that your system is not well equilibrated. 
> For more information and tips for troubleshooting, please check the GROMACS 
> website at http://www.gromacs.org/Documentation/Errors 
> 
> 
> 
> How can I fix the system, when the energy minimization step cannot? 
> 

You haven't provided any information about the force field you're using, .mdp 
settings, etc. so there's nothing to go on. If this is an immediate failure, 
visualize your starting coordinates because there's something wrong. Otherwise, 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-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] Genion

2017-06-22 Thread Mark Abraham

Hi,

The error message has a helpful URL that'll take you to the same advice
that we give several times a week on here :-)

Mark

On Thu, 22 Jun 2017 14:27 Sergio Manzetti 
wrote:

> Thanks, Worked out. Now I got a note saying:
>
> NOTE 1 [file em.mdp]:
> The group cutoff scheme is deprecated since GROMACS 5.0 and will be
> removed in a future release when all interaction forms are supported for
> the verlet scheme. The verlet scheme already scales better, and it is
> compatible with GPUs and other accelerators.
>
>
>
> Fatal error:
> 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
>
> How can I fix the system, when the energy minimization step cannot?
>
>
> Sergio
>
>
> Sergio Manzetti
>
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
>
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
> |   ]
> Midtun
> 6894 Vangsnes
> Norge
> Org.nr. 911 659 654
> Tlf: +47 57695621
> [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ |
> Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [
> http://www.phap.no/ | FAP ]
>
>
>
> From: "Justin Lemkul" 
> To: "gmx-users" 
> Sent: Thursday, June 22, 2017 2:21:17 PM
> Subject: Re: [gmx-users] Genion
>
> On 6/22/17 8:14 AM, Sergio Manzetti wrote:
> > OK, now I treied writing Na Cl and not NA and CL and get:
> >
>
> This is what you did before, so naturally you get the same thing.
>
> > Na)
> > Warning: atom name 11966 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> > Warning: atom name 11967 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> > Warning: atom name 11968 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> > Warning: atom name 11969 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> > Warning: atom name 11970 in topol.top and dna_solv_NaCl.gro does not
> match (NA - Na)
> >
>
> As I said, using mixed case is incorrect. The [moleculetype] entries in
> ions.itp expect all caps. Use all caps.
>
> -Justin
>
> >
> >
> >
> >
> > Sergio Manzetti
> >
> > [ http://www.fjordforsk.no/logo_hr2.jpg ]
> >
> > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [
> http://www.fjordforsk.no/ | ]
> > Midtun
> > 6894 Vangsnes
> > Norge
> > Org.nr. 911 659 654
> > Tlf: +47 57695621
> > [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ |
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/
> | FAP ]
> >
> >
> >
> > From: "Justin Lemkul" 
> > To: "gmx-users" 
> > Sent: Thursday, June 22, 2017 2:09:02 PM
> > Subject: Re: [gmx-users] Genion
> >
> > On 6/22/17 7:30 AM, Sergio Manzetti wrote:
> >> Hi, the procedure as defined by Juistin worked out well. However, a new
> problem has occurred. At mdrun for the minimization, I get:
> >>
> >> ---
> >> Program gmx mdrun, VERSION 5.1.2
> >> Source code file:
> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/ewald/pme-redistribute.cpp,
> line: 276
> >>
> >> Fatal error:
> >> 1 particles communicated to PME rank 3 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> >> This usually means that your system is not well equilibrated.
> >> For more information and tips for troubleshooting, please check the
> GROMACS
> >> website at http://www.gromacs.org/Documentation/Errors
> >>
> >>
> >> This may be caused by the solvent replacement of genion by Na Cl:
> >>
> >>
> >>
> >> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision)
> >> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision)
> >> Will try to add 130 Na ions and 90 Cl ions.
> >> Select a continuous group of solvent molecules
> >> Group 0 ( System) has 98254 elements
> >> Group 1 ( DNA) has 1333 elements
> >> Group 2 ( Water) has 96921 elements
> >> Group 3 ( SOL) has 96921 elements
> >> Group 4 ( non-Water) has 1333 elements
> >> Select a group: 3
> >> Selected 3: 'SOL'
> >> Number of (3-atomic) solvent molecules: 32307
> >> Replacing solvent molecule 3244 (atom 11065) with Na
> >> Replacing solvent molecule 8993 (atom 28312) with Na
> >> Replacing solvent molecule 7088 (atom 22597) with Na
> >> Replacing solvent molecule 29442 (atom 89659) with Na
> >> Replacing solvent molecule 30079 (atom 91570) with Na
> >> Replacing solvent molecule 5128 (atom 16717) with Na
> >> Replacing solvent molecule 10705 (atom 33448) with Na
> >> Replacing solvent molecule 1418 (atom 5587) with Na
> >> Replacing solvent molecule 6608 (atom 21157) with Na
> >> Replacing solvent molecule 28124 (atom 85705) with Na
> >> Replacing solvent molecule 5440

Re: [gmx-users] Genion

2017-06-22 Thread Justin Lemkul




On 6/22/17 8:22 AM, Sergio Manzetti wrote:

Thanks, Worked out. Now I got a note saying:

NOTE 1 [file em.mdp]:
The group cutoff scheme is deprecated since GROMACS 5.0 and will be
removed in a future release when all interaction forms are supported for
the verlet scheme. The verlet scheme already scales better, and it is
compatible with GPUs and other accelerators.



Fatal error:
1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out 
of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



How can I fix the system, when the energy minimization step cannot?



You haven't provided any information about the force field you're using, .mdp 
settings, etc. so there's nothing to go on.  If this is an immediate failure, 
visualize your starting coordinates because there's something wrong. Otherwise, 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System


-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

==
--
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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Re: [gmx-users] Genion

2017-06-22 Thread Sergio Manzetti

Thanks, Worked out. Now I got a note saying: 

NOTE 1 [file em.mdp]: 
The group cutoff scheme is deprecated since GROMACS 5.0 and will be 
removed in a future release when all interaction forms are supported for 
the verlet scheme. The verlet scheme already scales better, and it is 
compatible with GPUs and other accelerators. 



Fatal error: 
1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out 
of the domain decomposition cell of their charge group in dimension x. 
This usually means that your system is not well equilibrated. 
For more information and tips for troubleshooting, please check the GROMACS 
website at http://www.gromacs.org/Documentation/Errors 



How can I fix the system, when the energy minimization step cannot? 


Sergio 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Thursday, June 22, 2017 2:21:17 PM 
Subject: Re: [gmx-users] Genion 

On 6/22/17 8:14 AM, Sergio Manzetti wrote: 
> OK, now I treied writing Na Cl and not NA and CL and get: 
> 

This is what you did before, so naturally you get the same thing. 

> Na) 
> Warning: atom name 11966 in topol.top and dna_solv_NaCl.gro does not match 
> (NA - Na) 
> Warning: atom name 11967 in topol.top and dna_solv_NaCl.gro does not match 
> (NA - Na) 
> Warning: atom name 11968 in topol.top and dna_solv_NaCl.gro does not match 
> (NA - Na) 
> Warning: atom name 11969 in topol.top and dna_solv_NaCl.gro does not match 
> (NA - Na) 
> Warning: atom name 11970 in topol.top and dna_solv_NaCl.gro does not match 
> (NA - Na) 
> 

As I said, using mixed case is incorrect. The [moleculetype] entries in 
ions.itp expect all caps. Use all caps. 

-Justin 

> 
> 
> 
> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | 
> FAP ] 
> 
> 
> 
> From: "Justin Lemkul"  
> To: "gmx-users"  
> Sent: Thursday, June 22, 2017 2:09:02 PM 
> Subject: Re: [gmx-users] Genion 
> 
> On 6/22/17 7:30 AM, Sergio Manzetti wrote: 
>> Hi, the procedure as defined by Juistin worked out well. However, a new 
>> problem has occurred. At mdrun for the minimization, I get: 
>> 
>> --- 
>> Program gmx mdrun, VERSION 5.1.2 
>> Source code file: 
>> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/ewald/pme-redistribute.cpp, 
>> line: 276 
>> 
>> Fatal error: 
>> 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off 
>> out of the domain decomposition cell of their charge group in dimension x. 
>> This usually means that your system is not well equilibrated. 
>> For more information and tips for troubleshooting, please check the GROMACS 
>> website at http://www.gromacs.org/Documentation/Errors 
>> 
>> 
>> This may be caused by the solvent replacement of genion by Na Cl: 
>> 
>> 
>> 
>> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision) 
>> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision) 
>> Will try to add 130 Na ions and 90 Cl ions. 
>> Select a continuous group of solvent molecules 
>> Group 0 ( System) has 98254 elements 
>> Group 1 ( DNA) has 1333 elements 
>> Group 2 ( Water) has 96921 elements 
>> Group 3 ( SOL) has 96921 elements 
>> Group 4 ( non-Water) has 1333 elements 
>> Select a group: 3 
>> Selected 3: 'SOL' 
>> Number of (3-atomic) solvent molecules: 32307 
>> Replacing solvent molecule 3244 (atom 11065) with Na 
>> Replacing solvent molecule 8993 (atom 28312) with Na 
>> Replacing solvent molecule 7088 (atom 22597) with Na 
>> Replacing solvent molecule 29442 (atom 89659) with Na 
>> Replacing solvent molecule 30079 (atom 91570) with Na 
>> Replacing solvent molecule 5128 (atom 16717) with Na 
>> Replacing solvent molecule 10705 (atom 33448) with Na 
>> Replacing solvent molecule 1418 (atom 5587) with Na 
>> Replacing solvent molecule 6608 (atom 21157) with Na 
>> Replacing solvent molecule 28124 (atom 85705) with Na 
>> Replacing solvent molecule 5440 (atom 17653) with Na 
>> Replacing solvent molecule 31518 (atom 95887) with Na 
>> Replacing solvent molecule 16384 (atom 50485) with Na 
>> Replacing solvent molecule 17675 (atom 54358) with Na 
>> Replacing solvent molecule 23446 (atom 71671) with Na 
>> Replacing solvent molecule 15659 (atom 48310) with Na 
>> Replacing solvent

Re: [gmx-users] Genion

2017-06-22 Thread Justin Lemkul




On 6/22/17 8:14 AM, Sergio Manzetti wrote:

OK, now I treied writing Na Cl and not NA and CL and get:



This is what you did before, so naturally you get the same thing.


Na)
Warning: atom name 11966 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 11967 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 11968 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 11969 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 11970 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)



As I said, using mixed case is incorrect.  The [moleculetype] entries in 
ions.itp expect all caps.  Use all caps.


-Justin






Sergio Manzetti

[ http://www.fjordforsk.no/logo_hr2.jpg ]

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ]



From: "Justin Lemkul" 
To: "gmx-users" 
Sent: Thursday, June 22, 2017 2:09:02 PM
Subject: Re: [gmx-users] Genion

On 6/22/17 7:30 AM, Sergio Manzetti wrote:

Hi, the procedure as defined by Juistin worked out well. However, a new problem 
has occurred. At mdrun for the minimization, I get:

---
Program gmx mdrun, VERSION 5.1.2
Source code file: 
/build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/ewald/pme-redistribute.cpp, 
line: 276

Fatal error:
1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out 
of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


This may be caused by the solvent replacement of genion by Na Cl:



Reading file dna_solv.tpr, VERSION 5.1.2 (single precision)
Reading file dna_solv.tpr, VERSION 5.1.2 (single precision)
Will try to add 130 Na ions and 90 Cl ions.
Select a continuous group of solvent molecules
Group 0 ( System) has 98254 elements
Group 1 ( DNA) has 1333 elements
Group 2 ( Water) has 96921 elements
Group 3 ( SOL) has 96921 elements
Group 4 ( non-Water) has 1333 elements
Select a group: 3
Selected 3: 'SOL'
Number of (3-atomic) solvent molecules: 32307
Replacing solvent molecule 3244 (atom 11065) with Na
Replacing solvent molecule 8993 (atom 28312) with Na
Replacing solvent molecule 7088 (atom 22597) with Na
Replacing solvent molecule 29442 (atom 89659) with Na
Replacing solvent molecule 30079 (atom 91570) with Na
Replacing solvent molecule 5128 (atom 16717) with Na
Replacing solvent molecule 10705 (atom 33448) with Na
Replacing solvent molecule 1418 (atom 5587) with Na
Replacing solvent molecule 6608 (atom 21157) with Na
Replacing solvent molecule 28124 (atom 85705) with Na
Replacing solvent molecule 5440 (atom 17653) with Na
Replacing solvent molecule 31518 (atom 95887) with Na
Replacing solvent molecule 16384 (atom 50485) with Na
Replacing solvent molecule 17675 (atom 54358) with Na
Replacing solvent molecule 23446 (atom 71671) with Na
Replacing solvent molecule 15659 (atom 48310) with Na
Replacing solvent molecule 18442 (atom 56659) with Na
Replacing solvent molecule 23777 (atom 72664) with Na
Replacing solvent molecule 5965 (atom 19228) with Na
Replacing solvent molecule 15375 (atom 47458) with Na
Replacing solvent molecule 30985 (atom 94288) with Na
Replacing solvent molecule 19076 (atom 58561) with Na
Replacing solvent molecule 18065 (atom 55528) with Na
Replacing solvent molecule 22711 (atom 69466) with Na
Replacing solvent molecule 27097 (atom 82624) with Na
Replacing solvent molecule 21561 (atom 66016) with Na
Replacing solvent molecule 18592 (atom 57109) with Na
Replacing solvent molecule 22174 (atom 67855) with Na
Replacing solvent molecule 17888 (atom 54997) with Na
Replacing solvent molecule 13005 (atom 40348) with Na
Replacing solvent molecule 3481 (atom 11776) with Na
Replacing solvent molecule 22603 (atom 69142) with Na
Replacing solvent molecule 9899 (atom 31030) with Na
Replacing solvent molecule 3438 (atom 11647) with Na
Replacing solvent molecule 12180 (atom 37873) with Na
Replacing solvent molecule 32219 (atom 97990) with Na
Replacing solvent molecule 23159 (atom 70810) with Na
Replacing solvent molecule 27929 (atom 85120) with Na


which then reflects on grompp as:



Setting the LD random seed to 3274024379
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'DNA_chain_E'
Excluding 3 bonded neighbours molecule type 'DNA_chain_F'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded

Re: [gmx-users] Genion

2017-06-22 Thread Sergio Manzetti

OK, now I treied writing Na Cl and not NA and CL and get: 

Na) 
Warning: atom name 11966 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 11967 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 11968 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 11969 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 11970 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 





Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Thursday, June 22, 2017 2:09:02 PM 
Subject: Re: [gmx-users] Genion 

On 6/22/17 7:30 AM, Sergio Manzetti wrote: 
> Hi, the procedure as defined by Juistin worked out well. However, a new 
> problem has occurred. At mdrun for the minimization, I get: 
> 
> --- 
> Program gmx mdrun, VERSION 5.1.2 
> Source code file: 
> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/ewald/pme-redistribute.cpp, 
> line: 276 
> 
> Fatal error: 
> 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off 
> out of the domain decomposition cell of their charge group in dimension x. 
> This usually means that your system is not well equilibrated. 
> For more information and tips for troubleshooting, please check the GROMACS 
> website at http://www.gromacs.org/Documentation/Errors 
> 
> 
> This may be caused by the solvent replacement of genion by Na Cl: 
> 
> 
> 
> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision) 
> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision) 
> Will try to add 130 Na ions and 90 Cl ions. 
> Select a continuous group of solvent molecules 
> Group 0 ( System) has 98254 elements 
> Group 1 ( DNA) has 1333 elements 
> Group 2 ( Water) has 96921 elements 
> Group 3 ( SOL) has 96921 elements 
> Group 4 ( non-Water) has 1333 elements 
> Select a group: 3 
> Selected 3: 'SOL' 
> Number of (3-atomic) solvent molecules: 32307 
> Replacing solvent molecule 3244 (atom 11065) with Na 
> Replacing solvent molecule 8993 (atom 28312) with Na 
> Replacing solvent molecule 7088 (atom 22597) with Na 
> Replacing solvent molecule 29442 (atom 89659) with Na 
> Replacing solvent molecule 30079 (atom 91570) with Na 
> Replacing solvent molecule 5128 (atom 16717) with Na 
> Replacing solvent molecule 10705 (atom 33448) with Na 
> Replacing solvent molecule 1418 (atom 5587) with Na 
> Replacing solvent molecule 6608 (atom 21157) with Na 
> Replacing solvent molecule 28124 (atom 85705) with Na 
> Replacing solvent molecule 5440 (atom 17653) with Na 
> Replacing solvent molecule 31518 (atom 95887) with Na 
> Replacing solvent molecule 16384 (atom 50485) with Na 
> Replacing solvent molecule 17675 (atom 54358) with Na 
> Replacing solvent molecule 23446 (atom 71671) with Na 
> Replacing solvent molecule 15659 (atom 48310) with Na 
> Replacing solvent molecule 18442 (atom 56659) with Na 
> Replacing solvent molecule 23777 (atom 72664) with Na 
> Replacing solvent molecule 5965 (atom 19228) with Na 
> Replacing solvent molecule 15375 (atom 47458) with Na 
> Replacing solvent molecule 30985 (atom 94288) with Na 
> Replacing solvent molecule 19076 (atom 58561) with Na 
> Replacing solvent molecule 18065 (atom 55528) with Na 
> Replacing solvent molecule 22711 (atom 69466) with Na 
> Replacing solvent molecule 27097 (atom 82624) with Na 
> Replacing solvent molecule 21561 (atom 66016) with Na 
> Replacing solvent molecule 18592 (atom 57109) with Na 
> Replacing solvent molecule 22174 (atom 67855) with Na 
> Replacing solvent molecule 17888 (atom 54997) with Na 
> Replacing solvent molecule 13005 (atom 40348) with Na 
> Replacing solvent molecule 3481 (atom 11776) with Na 
> Replacing solvent molecule 22603 (atom 69142) with Na 
> Replacing solvent molecule 9899 (atom 31030) with Na 
> Replacing solvent molecule 3438 (atom 11647) with Na 
> Replacing solvent molecule 12180 (atom 37873) with Na 
> Replacing solvent molecule 32219 (atom 97990) with Na 
> Replacing solvent molecule 23159 (atom 70810) with Na 
> Replacing solvent molecule 27929 (atom 85120) with Na 
> 
> 
> which then reflects on grompp as: 
> 
> 
> 
> Setting the LD random seed to 3274024379 
> Generated 2211 of the 2211 non-bonded parameter combinations 
> Generating 1-4 interactions: fudge = 0.5 
> Generated 2211 of the 2211 1-4 parameter combinations 
> Excluding 3 bonded neighbours molecule type 'DNA_chain_E' 
> Excluding 3 bonded neighbours molecule type 'DNA_chain_F' 
> Excluding 2 bonded neighbours molecule type 'SOL' 
>

Re: [gmx-users] Simulation of Carbon nanotube

2017-06-22 Thread Justin Lemkul




On 6/22/17 6:59 AM, Nikhil Maroli wrote:

Dear Justin,
I have generated topology for CNT using gmx x2top. There is cyclic peptide
nanotube wrapped over the CNT (eight CP rings in equal intervals) otherwise
let's say, CNT is inserted into the Cyclic peptide nanotube. I wanted to
put the whole system into the lipid bilayer. I was using charmm-gui for the
input generator since it provides easy hand on CPN, So is it possible to
convert the CNT topology which generated with gmx x2top to 'Topology and
Parameters' for charmm-gui (*.rtf and *.prm)?


Possibly, but I've never tried it.  Assuming it's an "infinite" molecule, the 
periodic bonding could be tricky.  You may just want to build the membrane and 
then write a little script to carve out a cylinder of suitable size later, and 
overlay your existing coordinates.  Probably a lot less effort, in the end.


-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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Genion

2017-06-22 Thread Justin Lemkul




On 6/22/17 7:30 AM, Sergio Manzetti wrote:

Hi, the procedure as defined by Juistin worked out well. However, a new problem 
has occurred. At mdrun for the minimization, I get:

---
Program gmx mdrun, VERSION 5.1.2
Source code file: 
/build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/ewald/pme-redistribute.cpp, 
line: 276

Fatal error:
1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out 
of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


This may be caused by the solvent replacement of genion by Na Cl:



Reading file dna_solv.tpr, VERSION 5.1.2 (single precision)
Reading file dna_solv.tpr, VERSION 5.1.2 (single precision)
Will try to add 130 Na ions and 90 Cl ions.
Select a continuous group of solvent molecules
Group 0 ( System) has 98254 elements
Group 1 ( DNA) has 1333 elements
Group 2 ( Water) has 96921 elements
Group 3 ( SOL) has 96921 elements
Group 4 ( non-Water) has 1333 elements
Select a group: 3
Selected 3: 'SOL'
Number of (3-atomic) solvent molecules: 32307
Replacing solvent molecule 3244 (atom 11065) with Na
Replacing solvent molecule 8993 (atom 28312) with Na
Replacing solvent molecule 7088 (atom 22597) with Na
Replacing solvent molecule 29442 (atom 89659) with Na
Replacing solvent molecule 30079 (atom 91570) with Na
Replacing solvent molecule 5128 (atom 16717) with Na
Replacing solvent molecule 10705 (atom 33448) with Na
Replacing solvent molecule 1418 (atom 5587) with Na
Replacing solvent molecule 6608 (atom 21157) with Na
Replacing solvent molecule 28124 (atom 85705) with Na
Replacing solvent molecule 5440 (atom 17653) with Na
Replacing solvent molecule 31518 (atom 95887) with Na
Replacing solvent molecule 16384 (atom 50485) with Na
Replacing solvent molecule 17675 (atom 54358) with Na
Replacing solvent molecule 23446 (atom 71671) with Na
Replacing solvent molecule 15659 (atom 48310) with Na
Replacing solvent molecule 18442 (atom 56659) with Na
Replacing solvent molecule 23777 (atom 72664) with Na
Replacing solvent molecule 5965 (atom 19228) with Na
Replacing solvent molecule 15375 (atom 47458) with Na
Replacing solvent molecule 30985 (atom 94288) with Na
Replacing solvent molecule 19076 (atom 58561) with Na
Replacing solvent molecule 18065 (atom 55528) with Na
Replacing solvent molecule 22711 (atom 69466) with Na
Replacing solvent molecule 27097 (atom 82624) with Na
Replacing solvent molecule 21561 (atom 66016) with Na
Replacing solvent molecule 18592 (atom 57109) with Na
Replacing solvent molecule 22174 (atom 67855) with Na
Replacing solvent molecule 17888 (atom 54997) with Na
Replacing solvent molecule 13005 (atom 40348) with Na
Replacing solvent molecule 3481 (atom 11776) with Na
Replacing solvent molecule 22603 (atom 69142) with Na
Replacing solvent molecule 9899 (atom 31030) with Na
Replacing solvent molecule 3438 (atom 11647) with Na
Replacing solvent molecule 12180 (atom 37873) with Na
Replacing solvent molecule 32219 (atom 97990) with Na
Replacing solvent molecule 23159 (atom 70810) with Na
Replacing solvent molecule 27929 (atom 85120) with Na


which then reflects on grompp as:



Setting the LD random seed to 3274024379
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'DNA_chain_E'
Excluding 3 bonded neighbours molecule type 'DNA_chain_F'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'
Excluding 1 bonded neighbours molecule type 'CL'
Warning: atom name 97595 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97596 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97597 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97598 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97599 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97600 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97601 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97602 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97603 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97604 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97605 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97606 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97607 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na)
Warning: atom name 97608 in topol.top and dna_solv_NaCl.gro

Re: [gmx-users] Genion

2017-06-22 Thread Sergio Manzetti

Hi, the procedure as defined by Juistin worked out well. However, a new problem 
has occurred. At mdrun for the minimization, I get: 

--- 
Program gmx mdrun, VERSION 5.1.2 
Source code file: 
/build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/ewald/pme-redistribute.cpp, 
line: 276 

Fatal error: 
1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out 
of the domain decomposition cell of their charge group in dimension x. 
This usually means that your system is not well equilibrated. 
For more information and tips for troubleshooting, please check the GROMACS 
website at http://www.gromacs.org/Documentation/Errors 


This may be caused by the solvent replacement of genion by Na Cl: 



Reading file dna_solv.tpr, VERSION 5.1.2 (single precision) 
Reading file dna_solv.tpr, VERSION 5.1.2 (single precision) 
Will try to add 130 Na ions and 90 Cl ions. 
Select a continuous group of solvent molecules 
Group 0 ( System) has 98254 elements 
Group 1 ( DNA) has 1333 elements 
Group 2 ( Water) has 96921 elements 
Group 3 ( SOL) has 96921 elements 
Group 4 ( non-Water) has 1333 elements 
Select a group: 3 
Selected 3: 'SOL' 
Number of (3-atomic) solvent molecules: 32307 
Replacing solvent molecule 3244 (atom 11065) with Na 
Replacing solvent molecule 8993 (atom 28312) with Na 
Replacing solvent molecule 7088 (atom 22597) with Na 
Replacing solvent molecule 29442 (atom 89659) with Na 
Replacing solvent molecule 30079 (atom 91570) with Na 
Replacing solvent molecule 5128 (atom 16717) with Na 
Replacing solvent molecule 10705 (atom 33448) with Na 
Replacing solvent molecule 1418 (atom 5587) with Na 
Replacing solvent molecule 6608 (atom 21157) with Na 
Replacing solvent molecule 28124 (atom 85705) with Na 
Replacing solvent molecule 5440 (atom 17653) with Na 
Replacing solvent molecule 31518 (atom 95887) with Na 
Replacing solvent molecule 16384 (atom 50485) with Na 
Replacing solvent molecule 17675 (atom 54358) with Na 
Replacing solvent molecule 23446 (atom 71671) with Na 
Replacing solvent molecule 15659 (atom 48310) with Na 
Replacing solvent molecule 18442 (atom 56659) with Na 
Replacing solvent molecule 23777 (atom 72664) with Na 
Replacing solvent molecule 5965 (atom 19228) with Na 
Replacing solvent molecule 15375 (atom 47458) with Na 
Replacing solvent molecule 30985 (atom 94288) with Na 
Replacing solvent molecule 19076 (atom 58561) with Na 
Replacing solvent molecule 18065 (atom 55528) with Na 
Replacing solvent molecule 22711 (atom 69466) with Na 
Replacing solvent molecule 27097 (atom 82624) with Na 
Replacing solvent molecule 21561 (atom 66016) with Na 
Replacing solvent molecule 18592 (atom 57109) with Na 
Replacing solvent molecule 22174 (atom 67855) with Na 
Replacing solvent molecule 17888 (atom 54997) with Na 
Replacing solvent molecule 13005 (atom 40348) with Na 
Replacing solvent molecule 3481 (atom 11776) with Na 
Replacing solvent molecule 22603 (atom 69142) with Na 
Replacing solvent molecule 9899 (atom 31030) with Na 
Replacing solvent molecule 3438 (atom 11647) with Na 
Replacing solvent molecule 12180 (atom 37873) with Na 
Replacing solvent molecule 32219 (atom 97990) with Na 
Replacing solvent molecule 23159 (atom 70810) with Na 
Replacing solvent molecule 27929 (atom 85120) with Na 


which then reflects on grompp as: 



Setting the LD random seed to 3274024379 
Generated 2211 of the 2211 non-bonded parameter combinations 
Generating 1-4 interactions: fudge = 0.5 
Generated 2211 of the 2211 1-4 parameter combinations 
Excluding 3 bonded neighbours molecule type 'DNA_chain_E' 
Excluding 3 bonded neighbours molecule type 'DNA_chain_F' 
Excluding 2 bonded neighbours molecule type 'SOL' 
Excluding 1 bonded neighbours molecule type 'NA' 
Excluding 1 bonded neighbours molecule type 'CL' 
Warning: atom name 97595 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97596 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97597 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97598 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97599 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97600 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97601 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97602 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97603 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97604 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97605 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97606 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name 97607 in topol.top and dna_solv_NaCl.gro does not match (NA 
- Na) 
Warning: atom name

Re: [gmx-users] How to perform final MD simulation after extending a NPT simulation

2017-06-22 Thread Mark Abraham

Hi,

On Wed, Jun 21, 2017 at 3:24 AM Adarsh V. K. 
wrote:

> Dear all,
>
> *I used following command to extend a NPT simulation*
>
> 1) gmx convert-tpr -s npt.tpr -extend 500 -o tpxout.tpr
> gmx mdrun -deffnm tpxout -cpi npt.cpt -v
>
> but the analysis " gmx energy -f  *tpxout*.edr -o pressure.xvg " shows only
> the extended part; How to append the extend part to previous cpt

trjcat and eneconv

> and
> continue to production MD ?
>

You don't want to append all your equilibration data and then your
production data. You're going to discard your equilibration period before
you analyse the data you produce...

---
> *Now to do a final MD simulation what command I should use?*
>
> 2) gmx grompp -f md.mdp -c npt.gro -t *npt.cpt* -p topol.top -n index.ndx
> -o md_0_1.tpr
> gmx mdrun -deffnm md_0_1 -v
>
> or
>
> 3) gmx grompp -f md.mdp -c npt.gro -t *tpxout.cpt* -p topol.top -n
> index.ndx -o md_0_1.tpr
> gmx mdrun -deffnm md_0_1 -v
>

These are identical except for the grompp -t, which controls what
configuration is written to the .tpr. Choose the one that makes sense for
the point from which you are trying to start.

Mark

*no need to combine; just use the third command to continue to MD
> simulation?*
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Re: [gmx-users] (no subject)

2017-06-22 Thread Mark Abraham

Hi,

I suggest you ask the authors of the tools, having checked their
documentation.

Mark

On Wed, Jun 21, 2017 at 6:36 AM Shivangi Agarwal <
shivangi.agarwal...@gmail.com> wrote:

> Hello all
>
> How to handle HS14 generated by ATB server in topology file?
>
>
> Regards
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Re: [gmx-users] positive potential energy

2017-06-22 Thread Mark Abraham

Hi,

On Thu, Jun 22, 2017 at 11:30 AM Emran Heshmati  wrote:

> Hi all
> I run two simulations on a 16 aa peptide under the same conditions
> (forcefield, simulation duration, ...) except the solvent in one of
> the simulations was TFE instead of water. The potential energy in the TFE
> containing system was positive (about 14 Kj/mol), while in water
> containing system was negative (about -7 Kj/mol). Is it normal? or some
> kind of error has occurred?
>

Seems normal. Models are typically not parameterized to have meaningful
total energies (but the differences and gradients are useful).

Mark

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Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

2017-06-22 Thread Mark Abraham

Hi,

On Thu, Jun 22, 2017 at 11:05 AM Diez Fernandez, Amanda <
amanda.die...@imperial.ac.uk> wrote:

> Hi Mark,
> Thank you for your reply.
>
> It is exactly the opposite though:

OK, I understood the images the other way around, without titles.

> for output_coordinates.gro which is the
> output from:
>
>  mdrun Š -c output_coordinates.gro
>
> it seems like atoms are diffusing out of the box.
>

They're just in whichever representation was convenient for mdrun, which as
I said is not intended to be the same as the output of any of the things
you might do with trjconv.

In the trajectory, I allow atoms to be seen to diffuse out of the box,
> using -pbc nojump, and I don¹t see them diffuse out (They stay within the
> unit cell, which is what I expect being a silica substrate at room
> temperature over a very short period of time).
>

Sure.

> So what puzzles me is why for the output of (mdrun -c) the atoms seem to
> diffuse out, specially so if I cannot see this in the trajectory.
>

mdrun will generally "make molecules whole" for -c, but otherwise doesn't
care. Implementing general triclininc 3D periodicity with domain
decomposition is a messy business. If you've written the final frame to the
trajectory, you can use trjconv to make the two outputs have the same
representation, but they still might be different by a translation.

Mark

Sorry if I didn¹t explain it very clearly last time.
>
> Thanks!
>
>
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Re: [gmx-users] Regarding the charge of the atom in the .rtp file

2017-06-22 Thread Mark Abraham

Hi,

I don't understand what you are asking. How does it relate to
parameterization methodology?

Mark

On Thu, Jun 22, 2017 at 7:20 AM Dilip H N  wrote:

> Thank you for reply..
>
> But how can i identify the molecule as methylamine (for example) since in
> the .rtp the molecule type is written as [MAM1]
> [ MAM1 ]
>   [ atoms ]
>N1 NG321-0.990  0
>C1 CG3AM2 -0.060  1
>   HN1 HGPAM20.390  2
>   HN2 HGPAM20.390  3
>   HC1 HGAAM20.090  4
>   HC2 HGAAM20.090  5
>   HC3 HGAAM20.090  6
>   [ bonds ]
>N1C1
>N1   HN1
>N1   HN2
>C1   HC1
>C1   HC2
>C1   HC3
> Is thr any hint such tht i can identify the molecule type written in .rtp
> file.??
> Or should i manually find it out..??... but in case of Glycine the molecule
> type is [GLY] which is easy to find
> How can i solve this issue..??
>
> Thank you...
>
>
>
>    Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
>
> On Wed, Jun 21, 2017 at 4:23 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > On Wed, Jun 21, 2017 at 11:59 AM Dilip H N 
> > wrote:
> >
> > > Hello all.
> > > 1] I want to knw how the charges are designated/assigned for the each
> > atoms
> > > in molecule in the .rtp file.  ie., as example for methylamine in
> CHARMM
> > > FF:-
> > >
> > > [ MAM1 ]
> > >   [ atoms ]
> > >   N1 NG321-0.990  0
> > >   C1 CG3AM2 -0.060  1
> > >  HN1 HGPAM20.390  2
> > >  HN2 HGPAM20.390  3
> > >  HC1 HGAAM20.090  4
> > >  HC2 HGAAM20.090  5
> > >  HC3 HGAAM20.090  6
> > >   [ bonds ]
> > >   N1C1
> > >   N1   HN1
> > >   N1   HN2
> > >   C1   HC1
> > >   C1   HC2
> > >   C1   HC3
> > >  ie how are the charges -0.990, -0.060, 0.390 etc., are assigned...
> > >
> >
> > The parameterization methodology is unique to each force field, and
> perhaps
> > to each tool that generates compatible topologies. You need to read that
> > documentation and literature to understand how they were derived.
> >
> >
> > > 2] and if i get the topology/itp file from the automated topology
> builder
> > > as in SwissParam for CHARMM forcefield, how can i confirm that the
> > charges
> > > assigned are exact..??
> > >
> >
> > You can see if they are correct in the sense of being a valid model of
> > reality by running a simulation and observing whether you can get
> > reasonable agreement with suitable e.g. experimental data.
> >
> > Mark
> >
> >
> > > Any help/suggestion is most welcome.
> > > Thank you...
> > > --
> > > With Best Regards,
> > >
> > > DILIP.H.N
> > > Ph.D Student
> > >
> > >
> > >
> > >    Sent with Mailtrack
> > > <
> > > https://mailtrack.io/install?source=signature=en;
> > referral=cy16f01.di...@nitk.edu.in=22
> > > >
> > > --
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> > >
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> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
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> > >
> > --
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> >
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
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Re: [gmx-users] Simulation of Carbon nanotube

2017-06-22 Thread Nikhil Maroli

Dear Justin,
I have generated topology for CNT using gmx x2top. There is cyclic peptide
nanotube wrapped over the CNT (eight CP rings in equal intervals) otherwise
let's say, CNT is inserted into the Cyclic peptide nanotube. I wanted to
put the whole system into the lipid bilayer. I was using charmm-gui for the
input generator since it provides easy hand on CPN, So is it possible to
convert the CNT topology which generated with gmx x2top to 'Topology and
Parameters' for charmm-gui (*.rtf and *.prm)?
Thanks in advance.
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[gmx-users] positive potential energy

2017-06-22 Thread Emran Heshmati

Hi all
I run two simulations on a 16 aa peptide under the same conditions
(forcefield, simulation duration, ...) except the solvent in one of
the simulations was TFE instead of water. The potential energy in the TFE
containing system was positive (about 14 Kj/mol), while in water
containing system was negative (about -7 Kj/mol). Is it normal? or some
kind of error has occurred?
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Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

2017-06-22 Thread Diez Fernandez, Amanda

Hi Mark, 
Thank you for your reply.

It is exactly the opposite though: for output_coordinates.gro which is the
output from:

 mdrun Š -c output_coordinates.gro

it seems like atoms are diffusing out of the box.

In the trajectory, I allow atoms to be seen to diffuse out of the box,
using -pbc nojump, and I don¹t see them diffuse out (They stay within the
unit cell, which is what I expect being a silica substrate at room
temperature over a very short period of time).

So what puzzles me is why for the output of (mdrun -c) the atoms seem to
diffuse out, specially so if I cannot see this in the trajectory.

Sorry if I didn¹t explain it very clearly last time.

Thanks!

On 22/06/2017, 06:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se"
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>   1. Re: Difference between output_coordinates.gro and
>  trajectory.xtc coordinates (Mark Abraham)
>   2. Re: (no subject) (Mark Abraham)
>   3. Re: puzzled by unexpected [ bonds ] section resulting from
>  running gmx x2top (Jose Borreguero)
>   4. Re: GROMACS and SIMtoEXP (Sanim Rahman)
>   5. Re: Regarding the charge of the atom in the .rtp file (Dilip H N)
>
>
>--
>
>Message: 1
>Date: Wed, 21 Jun 2017 17:29:53 +
>From: Mark Abraham 
>To: gmx-us...@gromacs.org
>Subject: Re: [gmx-users] Difference between output_coordinates.gro and
>   trajectory.xtc coordinates
>Message-ID:
>   
>Content-Type: text/plain; charset="UTF-8"
>
>Hi,
>
>On Wed, Jun 21, 2017 at 6:49 PM Diez Fernandez, Amanda <
>amanda.die...@imperial.ac.uk> wrote:
>
>> Hi Justin,
>> Thank you for your reply.
>>
>> Here are the links to the images of:
>> -the output coordinates
>> -and last frame of trajectory.
>>
>> Output coordinates which look wrong:
>> 
>>http://i1036.photobucket.com/albums/a443/amanda222lld/output_coordinates_
>>zp
>> stuqkgjd2.png
>> 
>>>_zpstuqkgjd2.png>
>>
>> Last frame from trajectory which looks OK:
>> 
>>http://i1036.photobucket.com/albums/a443/amanda222lld/last_frame_traj_zps
>>n2
>> 7nzusn.png
>> 
>>>sn27nzusn.png>
>>
>> For the last frame of the trajectory I used trjconv -pbc nojump to make
>> sure the atoms were not being wrapped around the box.
>
>
>That's what you're getting. See "gmx help trjconv" where it specifically
>says that "-pbc nojump" will lead to atoms appearing to diffuse out of the
>box.
>
>It seems like you want trjconv -pbc atom, so all the atoms are in the same
>box. That won't necessarily match what mdrun -c writes, either, because
>that is not something for which we have designed. There's an infinite
>number of equivalent representations of any system, and a large number of
>plausible representations that someone might want to use for different
>purposes, so we've left the choice to you, with the tools and
>documentation
>to get something that makes you happy :-)
>
>Mark
>
>
>--
>
>Message: 2
>Date: Wed, 21 Jun 2017 17:35:04 +
>From: Mark Abraham 
>To: gmx-us...@gromacs.org
>Subject: Re: [gmx-users] (no subject)
>Message-ID:
>   
>Content-Type: text/plain; charset="UTF-8"
>
>Hi,
>
>On Wed, Jun 21, 2017 at 4:32 PM Shivangi Agarwal <
>shivangi.agarwal...@gmail.com> wrote:
>
>> Hi
>> But it is broken. ..
>>
>
>Nope, it's just in one of the infinite number of equivalent
>representations
>of the same thing ;-) mdrun doesn't know that you want it to write a file
>where your protein and ligand and whatever strand are a cluster of things
>that you'd like it to render centered in the same periodic cell. That's
>what e.g. gmx trjconv -pbc cluster is useful for.
>
>strand with proline with three odr residues has been broken and visible...
>> i have Checked in vmd and pymol
>>
>
>Doesn't matter until you've said to a program "keep these things together"
>:-)
>
>Mark
>
>
>> On 21 Jun 2017 17:16, "Mark Abraham"

Re: [gmx-users] Pulling inside a channel to calculate the PMF

2017-06-22 Thread François-Régis Chalaoux

Hi Alex,

There is no confusion about the pulling that is only a preparation for
WHAM, but as you tell it you need to choose positions. These positions
could be choosen manually: if one choose to explore the static channel from
apo, then I'm agree, select the positions in the channel "in a bunch of
reasonably spaced spots along the curved "axis" of your channel, each
followed by equilibration and the production run, yielding the data useful
for WHAM". As you say, you need time and patience. Could PLUMED (or
somethoing else) /Gromacs be used to automate this ?

On the other side, this channel come from a static APO structure and the
reality of this channel is tiedous, so why not discover dynamically the
channel and run the next equilibration and the production run on the fly, could
PLUMED (or somethoing else)/Gromacs  be used to automate this ? How to
discover the channel on the fly ? May be it is feasible to use simply the
coordinates of the channel discovered by MDPocket with a long classical MD
realized  previously on the apo/holo structure ?

FR.

2017-06-22 10:19 GMT+02:00 Alex :

> I think your problem is solvable with enough perseverance, but there may
> also be some confusion... The PMF calculation isn't based on the data
> obtained from an actual pull: the pulling rate in those simulations is set
> to zero. The reason for using pull code there is to pull (pun intended) the
> positions and/or forces. The initial structures, of course, is where e.g.
> Justin's tutorial uses pull along a straight line.
>
> However, if you have the time and patience, you could of course
> (manually?) put your ligand in a bunch of reasonably spaced spots along the
> curved "axis" of your channel, each followed by equilibration and the
> production run, yielding the data useful for WHAM.
>
> Hope this helps.
>
> Alex
>
>
> On 6/22/2017 2:05 AM, François-Régis Chalaoux wrote:
>
>> Hi everybody,
>>
>> I would like to pull a ligand in a channel from my protein and calculate
>> the PMF with Umbrella sampling. This channel is probably not linear and
>> thus have to be defined. Too much colisions appears along a simple one
>> axis
>> pulling and causing a catastrophic PMF calculation.
>>
>> Currently I'm working with Gromacs and I wondered if it is possible to
>> define statically or dynamically the coordinates for the center of the
>> channel and use it during the simulation (Pulling).
>>
>> One solution could be to define in the md_pull.mdp configuration file all
>> the transition points of my pathway through which my ligand must pass from
>> my APO structure determined with CAVER.
>> Instantiation of Gromacs parameters of md_pull.mdp is not enough clear for
>> me and PLUMED is may be a more direct solution. Currently I have no
>> experience with PLUMED but It seems on paper to be able.
>>
>> An other choice would be to define dynamically the channel center,
>> on-the-fly. PLUMED seems also capable to manage this sort of challenge but
>> once again I have no idea of the feasibility of a such work.
>>
>>
>> What do you think about this problem and of the tracks evoked above ?
>>
>>
>> Cheers, FR.
>>
>> *Pulling inside a channel to calculate the PMF*. Available from:
>> https://www.researchgate.net/post/Pulling_inside_a_channel_t
>> o_calculate_the_PMF#594b792648954cf7f2759a48
>> [accessed Jun 22, 2017].
>>
>
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Re: [gmx-users] Pulling inside a channel to calculate the PMF

2017-06-22 Thread Alex

I think your problem is solvable with enough perseverance, but there may
also be some confusion... The PMF calculation isn't based on the data
obtained from an actual pull: the pulling rate in those simulations is
set to zero. The reason for using pull code there is to pull (pun
intended) the positions and/or forces. The initial structures, of
course, is where e.g. Justin's tutorial uses pull along a straight line.

However, if you have the time and patience, you could of course
(manually?) put your ligand in a bunch of reasonably spaced spots along
the curved "axis" of your channel, each followed by equilibration and
the production run, yielding the data useful for WHAM.

Hope this helps.

Alex

On 6/22/2017 2:05 AM, François-Régis Chalaoux wrote:

Hi everybody,

I would like to pull a ligand in a channel from my protein and calculate
the PMF with Umbrella sampling. This channel is probably not linear and
thus have to be defined. Too much colisions appears along a simple one axis
pulling and causing a catastrophic PMF calculation.

Currently I'm working with Gromacs and I wondered if it is possible to
define statically or dynamically the coordinates for the center of the
channel and use it during the simulation (Pulling).

One solution could be to define in the md_pull.mdp configuration file all
the transition points of my pathway through which my ligand must pass from
my APO structure determined with CAVER.
Instantiation of Gromacs parameters of md_pull.mdp is not enough clear for
me and PLUMED is may be a more direct solution. Currently I have no
experience with PLUMED but It seems on paper to be able.

An other choice would be to define dynamically the channel center,
on-the-fly. PLUMED seems also capable to manage this sort of challenge but
once again I have no idea of the feasibility of a such work.

What do you think about this problem and of the tracks evoked above ?

Cheers, FR.

*Pulling inside a channel to calculate the PMF*. Available from:
https://www.researchgate.net/post/Pulling_inside_a_channel_to_calculate_the_PMF#594b792648954cf7f2759a48
[accessed Jun 22, 2017].

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[gmx-users] Pulling inside a channel to calculate the PMF

2017-06-22 Thread François-Régis Chalaoux

Hi everybody,

Currently I'm working with Gromacs and I wondered if it is possible to
define statically or dynamically the coordinates for the center of the
channel and use it during the simulation (Pulling).

What do you think about this problem and of the tracks evoked above ?

Cheers, FR.

*Pulling inside a channel to calculate the PMF*. Available from:
https://www.researchgate.net/post/Pulling_inside_a_channel_to_calculate_the_PMF#594b792648954cf7f2759a48
[accessed Jun 22, 2017].
--
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* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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