Re: [gmx-users] creating an "infinite" filament with editconf

[David van der Spoel]

On 07/12/15 14:06, Igaev, Maxim wrote:

Thanks David, thanks Vitaly for your answers.

@Vitaly: I also thought of this but the number of boundary atoms is too high. 
I'm afraid of introducing too many artifacts through the freezing.

@David: the default -dd option of mdrun says that gromacs will guess the optimal size of the 
domains. The same for -npme. Do you mean I should just vary the size of the domains to find an 
optimal decomposition grid? I rather thought that the parts of my dimer that are not in the box 
after editconf and genbox should be "put"/"wraped" back into the box somehow...


They do. The error you show is an implementation limitation that you 
have to learn how to work with. Try -npme 0 to start with.



Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] im Auftrag von 
David van der Spoel [sp...@xray.bmc.uu.se]
Gesendet: Montag, 7. Dezember 2015 12:26
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] creating an "infinite" filament with editconf

On 07/12/15 11:54, Igaev, Maxim wrote:

Dear Gromacs Users,

I have a protein dimer and would like to make an "infinite" filament out of it 
in z direction by using periodic boundary conditions and editconf. What I've done so far 
is

a) I've generated a topology for the dimer via

pdb2gmx -f dimer.pdb -o dim.gro -p dim.top -i dim.itp -water tip3p(force 
field was chosen interactively)

b) and created a periodic box by using editconf

editconf -f dim.gro -o dim_box.gro -bt triclinic -box 13.4 9.4 8.6 -center 6.7 
4.7 4.3


If I understand editconf correctly, it is supposed to create a periodic box of sizes 13.4 
x 9.4 x 8.6 and place the dimer's center of mass to (6.7, 4.7, 4.3) in this box. The size 
"8.6 nm" in z direction is the priodicity of my dimer, which means that the 
dimer doesn't fit completely into the box; some parts are sticking out. But this is 
needed to establish the periodicity.

When I try to equilibrate my system after sufficient energy minimization I get an error 
like "X particles communicated to PME node Y are more than a cell length out of the 
domain decomposition cell of their charge group", which means that my system is 
blowing up and I probably have a bad starting structure. I then checked whether my dimer 
has some steric clashes and it was fine. I could equilibrate my dimer in a normal water 
box (isolated dimer) and the simulation was just fine.


You're doing everything right, but will have to tweak the mdrun command
line settings to control the parallellization, in particular -dd and -npme

I wonder if I did something wrong during the editconf step. Should I wrap my 
dimer into the box after editconf so that I have no parts sticking out of the 
box?
In NAMD, a similar approach worked well - I just took my dimer and surrounded 
it by waters to have a box of sizes 13.4 x 9.4 x 8.6 and applied PBC to it. But 
how to do the same in GROMACS?


Thank you in advance for your help!

Cheers,
Maxim




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] RDF convergence

[Vitaly V. Chaban]

Mine converges.

What about box size?





On Fri, Dec 4, 2015 at 7:14 AM, Sudip Das  wrote:

> Hi,
>
> I am using g_rdf command (within gromacs-5.0.5) to calculate rdf as follow:
>
> g_rdf_mpi_d -f .xtc -n .ndx -o rdf -cn
>
> But the rdf is not getting converged to 1 exactly, rather it converges to
> approximately 1.03. Whenever I am calculating rdf like this for different
> sets of atoms, I am getting the same thing.
>
> Can anyone please tell me why is this happening and what is the way out?
> Any kind of help will be highly appreciated.
>
> Thanks in advanced,
>
> Sudip
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Re: [gmx-users] trajectory file

[mihammad roos]

Thank you all for your helpful answers. 


On Friday, December 4, 2015 4:35 PM, "Smith, Micholas D." 
 wrote:
 

 Although you should ask these type of questions to the VMD mailing list, since 
the trjaectory file format is typical of md simulations from gromacs, I'll give 
you a quick answer:

VMD needs to know the atom names/types in order to draw anything, these are not 
stored in the xtc file. Instead you need to load your geometry into vmd first 
(your .gro or .pdb file) for your system, and then load the trajectory as data 
into the "molecule" that vmd generates on screen. Alternatively, you can use 
gmx trjconv to convert your trajectory file from xtc to pdb (or gro) and read 
the multi-frame pdb or gro file into vmd (these files will have multiple 
frames, and the atom names, but can be fairly large in terms of disk space).

Also, welcome to the wonderful world of MD simulations!

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Friday, December 04, 2015 7:29 AM
To: gmx-us...@gromacs.org; mihammad roos
Subject: Re: [gmx-users] trajectory file

On 12/3/15 4:39 PM, mihammad roos wrote:
> Hi everybody,
>
>
>
> I ran the production MD and got the trajectory file (xtcformat) but as I’m 
> new to MD I don’t know how to visualize it. I opened it withvmd and it could 
> read the atoms and frames but didn’t show anything when playingthe frames. I 
> don’t know whether another program can do it or my xtc is notcorrect.
>

Try some VMD tutorials. Loading coordinates and subsequently trajectories (as
data for those initial coordinates) is covered in any basic tutorial. Ask VMD
questions on the VMD mailing list.

-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] (no subject)

[Justin Lemkul]

On 12/7/15 12:30 AM, Seera Suryanarayana wrote:

Dear Gromacs Users,

Sorry for the same mail again. I haven't provide sufficient information in
previous mail.

After energy minimization I have done nvt equilibrium for 1ns. It has taken
15 to 20 minutes when I done it previously. Same equilibrium I did day
before yesterday and it has take almost one day. I have used the same work
station in both equilibrium processes. I have used the following mdp file.
System consists 129 residue length protein and more the three 3,00,000
water molecules. Kindly check the mdp file and let me how to resolve this
long lasting processes.

I have used the following command:
mdrun -deffnm nvt -nt 4  means one MPI thread and 4 openMPP
threads.

topol.top info:
[ molecules ]
; Compound#mols
Protein_chain_A 1
SOL 300217
NA   11



You have a system of nearly 1 million(!) atoms.  For a 129-aa protein, this is 
wildly unnecessary unless the polypeptide is fully unfolded.  Is this the case? 
I would also never expect a run done on 4 cores, without a GPU, to ever achieve 
such performance like you claim above. Such a system will take many days to run 
on such hardware, not 15 minutes.


-Justin



define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 50; 2 * 50 = 1000 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 5000  ; save coordinates every 10.0 ps
nstvout = 5000  ; save velocities every 10.0 ps
nstenergy   = 5000  ; save energies every 10.0 ps
nstlog  = 5000  ; update log file every 10.0 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm= lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type = grid  ; search neighboring grid cells
nstlist = 10; 20 fs, largely irrelevant with
Verlet
rcoulomb= 1.0   ; short-range electrostatic cutoff
(in nm)
rvdw= 1.0   ; short-range van der Waals cutoff
(in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more
accurate
tau_t   = 0.1 0.1   ; time constant, in ps
ref_t   = 300 300   ; reference temperature, one for
each group, in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed


Thanks in advance
Surya
Graduate student
India.



--
==

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] creating an "infinite" filament with editconf

[Igaev, Maxim]

Dear Gromacs Users,

I have a protein dimer and would like to make an "infinite" filament out of it 
in z direction by using periodic boundary conditions and editconf. What I've 
done so far is

a) I've generated a topology for the dimer via

pdb2gmx -f dimer.pdb -o dim.gro -p dim.top -i dim.itp -water tip3p(force 
field was chosen interactively)

b) and created a periodic box by using editconf

editconf -f dim.gro -o dim_box.gro -bt triclinic -box 13.4 9.4 8.6 -center 6.7 
4.7 4.3


If I understand editconf correctly, it is supposed to create a periodic box of 
sizes 13.4 x 9.4 x 8.6 and place the dimer's center of mass to (6.7, 4.7, 4.3) 
in this box. The size "8.6 nm" in z direction is the priodicity of my dimer, 
which means that the dimer doesn't fit completely into the box; some parts are 
sticking out. But this is needed to establish the periodicity.

When I try to equilibrate my system after sufficient energy minimization I get 
an error like "X particles communicated to PME node Y are more than a cell 
length out of the domain decomposition cell of their charge group", which means 
that my system is blowing up and I probably have a bad starting structure. I 
then checked whether my dimer has some steric clashes and it was fine. I could 
equilibrate my dimer in a normal water box (isolated dimer) and the simulation 
was just fine.

I wonder if I did something wrong during the editconf step. Should I wrap my 
dimer into the box after editconf so that I have no parts sticking out of the 
box?
In NAMD, a similar approach worked well - I just took my dimer and surrounded 
it by waters to have a box of sizes 13.4 x 9.4 x 8.6 and applied PBC to it. But 
how to do the same in GROMACS?


Thank you in advance for your help!

Cheers,
Maxim
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Re: [gmx-users] creating an "infinite" filament with editconf

[David van der Spoel]

On 07/12/15 11:54, Igaev, Maxim wrote:

Dear Gromacs Users,

I have a protein dimer and would like to make an "infinite" filament out of it 
in z direction by using periodic boundary conditions and editconf. What I've done so far 
is

a) I've generated a topology for the dimer via

pdb2gmx -f dimer.pdb -o dim.gro -p dim.top -i dim.itp -water tip3p(force 
field was chosen interactively)

b) and created a periodic box by using editconf

editconf -f dim.gro -o dim_box.gro -bt triclinic -box 13.4 9.4 8.6 -center 6.7 
4.7 4.3


If I understand editconf correctly, it is supposed to create a periodic box of sizes 13.4 
x 9.4 x 8.6 and place the dimer's center of mass to (6.7, 4.7, 4.3) in this box. The size 
"8.6 nm" in z direction is the priodicity of my dimer, which means that the 
dimer doesn't fit completely into the box; some parts are sticking out. But this is 
needed to establish the periodicity.

When I try to equilibrate my system after sufficient energy minimization I get an error 
like "X particles communicated to PME node Y are more than a cell length out of the 
domain decomposition cell of their charge group", which means that my system is 
blowing up and I probably have a bad starting structure. I then checked whether my dimer 
has some steric clashes and it was fine. I could equilibrate my dimer in a normal water 
box (isolated dimer) and the simulation was just fine.

You're doing everything right, but will have to tweak the mdrun command 
line settings to control the parallellization, in particular -dd and -npme

I wonder if I did something wrong during the editconf step. Should I wrap my 
dimer into the box after editconf so that I have no parts sticking out of the 
box?
In NAMD, a similar approach worked well - I just took my dimer and surrounded 
it by waters to have a box of sizes 13.4 x 9.4 x 8.6 and applied PBC to it. But 
how to do the same in GROMACS?


Thank you in advance for your help!

Cheers,
Maxim




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] creating an "infinite" filament with editconf

[Vitaly V. Chaban]

Perhaps, it is technically easier to freeze the boundary atoms along the
periodic direction.




On Mon, Dec 7, 2015 at 9:26 AM, David van der Spoel 
wrote:

> On 07/12/15 11:54, Igaev, Maxim wrote:
>
>> Dear Gromacs Users,
>>
>> I have a protein dimer and would like to make an "infinite" filament out
>> of it in z direction by using periodic boundary conditions and editconf.
>> What I've done so far is
>>
>> a) I've generated a topology for the dimer via
>>
>> pdb2gmx -f dimer.pdb -o dim.gro -p dim.top -i dim.itp -water tip3p
>> (force field was chosen interactively)
>>
>> b) and created a periodic box by using editconf
>>
>> editconf -f dim.gro -o dim_box.gro -bt triclinic -box 13.4 9.4 8.6
>> -center 6.7 4.7 4.3
>>
>>
>> If I understand editconf correctly, it is supposed to create a periodic
>> box of sizes 13.4 x 9.4 x 8.6 and place the dimer's center of mass to (6.7,
>> 4.7, 4.3) in this box. The size "8.6 nm" in z direction is the priodicity
>> of my dimer, which means that the dimer doesn't fit completely into the
>> box; some parts are sticking out. But this is needed to establish the
>> periodicity.
>>
>> When I try to equilibrate my system after sufficient energy minimization
>> I get an error like "X particles communicated to PME node Y are more than a
>> cell length out of the domain decomposition cell of their charge group",
>> which means that my system is blowing up and I probably have a bad starting
>> structure. I then checked whether my dimer has some steric clashes and it
>> was fine. I could equilibrate my dimer in a normal water box (isolated
>> dimer) and the simulation was just fine.
>>
>> You're doing everything right, but will have to tweak the mdrun command
> line settings to control the parallellization, in particular -dd and -npme
>
>> I wonder if I did something wrong during the editconf step. Should I wrap
>> my dimer into the box after editconf so that I have no parts sticking out
>> of the box?
>> In NAMD, a similar approach worked well - I just took my dimer and
>> surrounded it by waters to have a box of sizes 13.4 x 9.4 x 8.6 and applied
>> PBC to it. But how to do the same in GROMACS?
>>
>>
>> Thank you in advance for your help!
>>
>> Cheers,
>> Maxim
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
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[gmx-users] xtc files

[mihammad roos]

Hello everybody,


 
I generated the initial structure by amber tools (the systemis consisted of a 
protein with some ions that the whole system is solvated inwater), then convert 
the top and crd files to gromacs topology and gro files(by using parmEd), and 
then run the equilibration and the production MD ingromacs. Now I have the 
trajectory file(.xtc file)( using“gmx trjconv” command) after running the 
production MD but I think thereis something wrong, when I load the xtc file in 
vmd the protein jump from oneposition to another position immediately. Actually 
I put the protein in thecenter when generating the system. Is it a trouble? 


I attached an image of the xtc file resulted from runningthe production MD 
(using gmx mdrun command notusing gmx trjconv command ), I think the bonds are 
not ok, but when loading thextc file resulted from gmx trjconv the bonds seems 
good. I don’t if there is aproblem or not


By the way I generated another system with a protein and somelipids around it 
which is solvated in water by amber tools (the box shape is spherical),when I 
convert it to gro and gromacs topology the gro file is ok (it isspherical) but 
after running the production MD when I open the trajectory filethe box is cubic 
and it is very confused. I want the system to be spherical.


 
Thank you, Mohammad.

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[gmx-users] water sorient

[xy21hb]

Dear all, I would like to calculate the water orientation near ubiqutin by 
gmx_sorient, gmx sorient -f md.trr -s md.tpr -o -no -ro -co -rc

first, the sord.xvg shows the angle (i.e. theta 1) between the vector1 (nearest 
heavy protein atom to water oxygen) and
vector 2 (water oxygen to the mid of of water hydrogen 1 and 2) is mostly 90 
degrees, isn't that weird?
I would expect water dipole more or less pointing to or away from the vector 1, 
depending on the charge of the heavy atom.

2nd, sori.xvg second column should be the distribution of cos (theta1), but it 
shows some value greater than 1.

Any ideas?

Thanks,

Yao
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Re: [gmx-users] xtc files

[Vitaly V. Chaban]

gromacs does not support "spherical" boxes, as well as I do not think this
would have been correct in view of PBC. No PBC will eventually lead to the
spherical cluster representation.





On Mon, Dec 7, 2015 at 10:07 AM, mihammad roos 
wrote:

> Hello everybody,
>
>
>
> I generated the initial structure by amber tools (the systemis consisted
> of a protein with some ions that the whole system is solvated inwater),
> then convert the top and crd files to gromacs topology and gro files(by
> using parmEd), and then run the equilibration and the production MD
> ingromacs. Now I have the trajectory file(.xtc file)( using“gmx trjconv”
> command) after running the production MD but I think thereis something
> wrong, when I load the xtc file in vmd the protein jump from oneposition to
> another position immediately. Actually I put the protein in thecenter when
> generating the system. Is it a trouble?
>
>
> I attached an image of the xtc file resulted from runningthe production MD
> (using gmx mdrun command notusing gmx trjconv command ), I think the bonds
> are not ok, but when loading thextc file resulted from gmx trjconv the
> bonds seems good. I don’t if there is aproblem or not
>
>
> By the way I generated another system with a protein and somelipids around
> it which is solvated in water by amber tools (the box shape is
> spherical),when I convert it to gro and gromacs topology the gro file is ok
> (it isspherical) but after running the production MD when I open the
> trajectory filethe box is cubic and it is very confused. I want the system
> to be spherical.
>
>
>
> Thank you, Mohammad.
>
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[gmx-users] LINCS WARNING

[masoud keramati]

Hi to all dear gmx users

during the Energy Minimization i got this warning in first few steps
after step 20
"step 20: Water molecule starting at atom 34209 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate."

but after 3021 steps it was converged to Fmax < 1000.

then i start the Equilibration and in the zero to 4 steps i got this:
"Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.018591, max 0.374857 (between atoms 2409 and 2411)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length"

in the step 5i got this and mdrun was terminate.
" Water molecule starting at atom 32146 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

WARNING: Listed nonbonded interaction between particles 2312 and 2326
at distance 4211.247 which is larger than the table limit 2.034 nm.

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

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


Segmentation fault (core dumped)"

my Equilibration is:

define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 500   ; save coordinates every 1.0 ps
nstvout = 500   ; save velocities every 1.0 ps
nstenergy   = 500   ; save energies every 1.0 ps
nstlog  = 500   ; update log file every 1.0 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm= lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type = grid  ; search neighboring grid cells
nstlist = 10; 20 fs, largely irrelevant with Verlet
rcoulomb= 1.0   ; short-range electrostatic cutoff (in 
nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in 
nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.135 ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = nose-hoover   ; modified Berendsen thermostat
tc-grps = system; two coupling groups - more accurate
tau_t   = 0.1 0.1   ; time constant, in ps
ref_t   = 300 300   ; reference temperature, one for each 
group, in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed



tnx for your help
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Re: [gmx-users] creating an "infinite" filament with editconf

[Igaev, Maxim]

Thanks David, thanks Vitaly for your answers.

@Vitaly: I also thought of this but the number of boundary atoms is too high. 
I'm afraid of introducing too many artifacts through the freezing.

@David: the default -dd option of mdrun says that gromacs will guess the 
optimal size of the domains. The same for -npme. Do you mean I should just vary 
the size of the domains to find an optimal decomposition grid? I rather thought 
that the parts of my dimer that are not in the box after editconf and genbox 
should be "put"/"wraped" back into the box somehow...




Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] im Auftrag von 
David van der Spoel [sp...@xray.bmc.uu.se]
Gesendet: Montag, 7. Dezember 2015 12:26
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] creating an "infinite" filament with editconf

On 07/12/15 11:54, Igaev, Maxim wrote:
> Dear Gromacs Users,
>
> I have a protein dimer and would like to make an "infinite" filament out of 
> it in z direction by using periodic boundary conditions and editconf. What 
> I've done so far is
>
> a) I've generated a topology for the dimer via
>
> pdb2gmx -f dimer.pdb -o dim.gro -p dim.top -i dim.itp -water tip3p(force 
> field was chosen interactively)
>
> b) and created a periodic box by using editconf
>
> editconf -f dim.gro -o dim_box.gro -bt triclinic -box 13.4 9.4 8.6 -center 
> 6.7 4.7 4.3
>
>
> If I understand editconf correctly, it is supposed to create a periodic box 
> of sizes 13.4 x 9.4 x 8.6 and place the dimer's center of mass to (6.7, 4.7, 
> 4.3) in this box. The size "8.6 nm" in z direction is the priodicity of my 
> dimer, which means that the dimer doesn't fit completely into the box; some 
> parts are sticking out. But this is needed to establish the periodicity.
>
> When I try to equilibrate my system after sufficient energy minimization I 
> get an error like "X particles communicated to PME node Y are more than a 
> cell length out of the domain decomposition cell of their charge group", 
> which means that my system is blowing up and I probably have a bad starting 
> structure. I then checked whether my dimer has some steric clashes and it was 
> fine. I could equilibrate my dimer in a normal water box (isolated dimer) and 
> the simulation was just fine.
>
You're doing everything right, but will have to tweak the mdrun command
line settings to control the parallellization, in particular -dd and -npme
> I wonder if I did something wrong during the editconf step. Should I wrap my 
> dimer into the box after editconf so that I have no parts sticking out of the 
> box?
> In NAMD, a similar approach worked well - I just took my dimer and surrounded 
> it by waters to have a box of sizes 13.4 x 9.4 x 8.6 and applied PBC to it. 
> But how to do the same in GROMACS?
>
>
> Thank you in advance for your help!
>
> Cheers,
> Maxim
>


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] using SPC water with Charmm FF

[jhon espinosa]

Hi allI finished running the 50 ns MD Simulation of a very large system (17 
Million atoms).It is a capsid in water. I used charmm FF for the protein and 
spc for the water.I am studying temperature triggered structural 
transitions.Since Charmm FF is build based on TIP3p water model, are my 
simulation results wrong?Is there any main issue that I should know?ThanksJohn



  
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Re: [gmx-users] using SPC water with Charmm FF

[Justin Lemkul]

On 12/7/15 6:59 PM, jhon espinosa wrote:

Hi allI finished running the 50 ns MD Simulation of a very large system (17 
Million atoms).It is a capsid in water. I used charmm FF for the protein and 
spc for the water.I am studying temperature triggered structural 
transitions.Since Charmm FF is build based on TIP3p water model, are my 
simulation results wrong?Is there any main issue that I should know?ThanksJohn



Sorry to say that is an invalid physical model.  The balance of forces will be 
totally wrong.


-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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