[gmx-users] CLOSED and DUPLICATED Re: Elegent way to continue md or trjcat continue trajectory

[Du, Yu]

Similar question has been answered by the following link:
http://thread.gmane.org/gmane.science.biology.gromacs.user/72772

The tinit option in .mdp file, which sets the starting time for continuous MD 
run.

If I use tinit in .mdp file, the second question will not exist. 

Yu


> -Original Messages-
> From: "Du, Yu" 
> Sent Time: 2017-09-29 12:12:00 (Friday)
> To: GMX-user 
> Cc: 
> Subject: [gmx-users] Elegent way to continue md or trjcat continue trajectory
> 
> Dear GMX Users, 
> 
> 
> I run MD after the previous MD and want to concatenate trajectories from 
> these N continuous MDs.
> 
> 
> 1) Do I need special time setting for the second MD to avoid the trjcat 
> confusing time setting?
> OR 2) Is there any ways to avoid the verbose interactive -setime, which needs 
> the N "c" input? 
> 
> Thanks.
> 
> 
> --
> Du, Yu
> PhD Student,
> Shanghai Institute of Organic Chemistry
> 345 Ling Ling Rd., Shanghai, China. 
> Zip: 200032, Tel: (86) 021 5492 5275
> -- 
> Gromacs Users mailing list
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> * Please search the archive at 
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--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275

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[gmx-users] Simulation in clusters -reg

[Meagha ramana kumar]

Hi gmx-users,

I was trying to run my simulation in core cluster in my institute. It is
showing the following error. But it works completely fine in my
personal laptop.

*the cluster error:-*

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.



*the gromacs error:-*

NOTE: Turning on dynamic load balancing


A list of missing interactions:
   LJ-14 of479 missing  1

Molecule type 'Macromolecule'
the first 10 missing interactions, except for exclusions:
   LJ-14 atoms  146  196   global   146   196

---
Program gmx mdrun, VERSION 5.1.2
Source code file:
/root/gromacs-5.1.2/src/gromacs/domdec/domdec_topology.cpp, line: 435

Fatal error:
1 of the 2886 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.18407 nm) or the two-body cut-off distance (2 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

thank you
Meagha
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[gmx-users] Memory allocation error in HPC

[Joydeep Munshi]

Dear Gromacs users,

I am trying to run a script in HPC using 80 CPUs from 4 nodes each with
128gb of memory available. while running the below mdrun for energy
minimisation process, I am getting memory allocation issue and the job is
being halted. Is there any issue with the way I am utilizing OpenMP and MPI
process in the code? What could be possible solutions.

Note while running the code in my workstation, I am not getting any error
and the energy minimization is converging quite well.

Part of the script given below:

*export OMP_NUM_THREADS=4*
*srun --ntasks-per-node=5 gmx_mpi mdrun $FLAGS -v -deffnm min_step000
-ntomp 4 >> mdrun.log 2>&1*


Error in mdrun.log is as below:

*Program gmx mdrun, VERSION 5.1.2*
*Source code file:
/home/alp514/source/corona2-build/gromacs-5.1.2/src/gromacs/utility/smalloc.c,
line: 227*

*Fatal error:*
*Not enough memory. Failed to realloc 302664 bytes for *f, *f=19367240*
*(called from file
/home/alp514/source/corona2-build/gromacs-5.1.2/src/gromacs/domdec/domdec.cpp,
line 1708)*
*For more information and tips for troubleshooting, please check the
GROMACS*
*website at http://www.gromacs.org/Documentation/Errors
*
*---*
*: Cannot allocate memory*
*Halting parallel program gmx mdrun on rank 27 out of 80*
*[cli_27]: aborting job:*
*application called MPI_Abort(MPI_COMM_WORLD, 1) - process 27*
*srun: error: sol-b410: task 27: Exited with exit code 1*
*[sol-b411:mpi_rank_47][handle_cqe] Send desc error in msg to 27,
wc_opcode=1*
*srun: error: sol-b411: task 47: Exited with exit code 252*
*[sol-b411:mpi_rank_47][handle_cqe] Msg from 27: wc.status=12,
wc.wr_id=0x331ff40, wc.opcode=1, vbuf->phead->type=0 =
MPIDI_CH3_PKT_EAGER_SEND*
*[sol-b411:mpi_rank_47][handle_cqe]
../mvapich2-2.1/src/mpid/ch3/channels/mrail/src/gen2/ibv_channel_manager.c:587:
[] Got completion with error 12, vendor code=0x81, dest rank=27*


Thanks in advance, Hoping suggestions on the resolution.


*Thanks and regards,*
*Joydeep Munshi,*
*Graduate Research Assistant,*
*Mechanical Engineering and Mechanics,*
*Lehigh University*
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[gmx-users] Elegent way to continue md or trjcat continue trajectory

[Du, Yu]

Dear GMX Users, 


I run MD after the previous MD and want to concatenate trajectories from these 
N continuous MDs.


1) Do I need special time setting for the second MD to avoid the trjcat 
confusing time setting?
OR 2) Is there any ways to avoid the verbose interactive -setime, which needs 
the N "c" input? 

Thanks.


--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275
-- 
Gromacs Users mailing list

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Re: [gmx-users] manually adding non-bonded interactions based on atom number to topology file

[Du, Yu]

Hi, 

Before the simulation of monomers polymerizing, you can try some tentative 
experiments, such dimerization and trimerization. If the simulation of 
trimerization succeeds, you really don't need the further experiment because 
the trimerization simulation is strong to support the further polymerization 
process because trimerization include the comformation change after 
dimerization and other important information.

Carefully design the size of the box to avoid the lenth of the polymer 
exceeding some dimension of the box whose size is fixed according to the preset 
seperated monomers, espesially in the case of trimer or larger numbers of 
monomers.

For PLUMED, 1) In the case of dimer, trimer or larger, you can use BIASVALUE to 
apply user-defined bias function between the A and B of different monomers. The 
bias function can choose to be that if the monomers are distant from each other 
the bias force is large, if near then the force is small to exclude the 
artifial bias effect.
2) In the case of dimer, you can also try the funnel metadynamics, which you 
can search for more information.

if you are simulating biological system, yours resembles the actin filament, 
you can search related simulation paper to check if there are published cases 
to study.

Cheers, 
Yu

> -Original Messages-
> From: "Amanda Parker" 
> Sent Time: 2017-09-29 01:10:20 (Friday)
> To: gmx-us...@gromacs.org
> Cc: 
> Subject: Re: [gmx-users] manually adding non-bonded interactions based on 
> atom number to topology file
> 
> Hi again,
> 
> For some reason I'm not getting your replies to my inbox, but I saw them in
> the Digest.
> 
> Wes-- I would like to see a sort of phase transition, yes, in which a
> number of monomers go from a disordered to ordered state. The ordered state
> will look something like AB-AB-AB-... where AB represents a monomer that
> has an A end and a B end (using Yu's description) that are identical, and
> the "-" indicates an attractive interaction.
> 
> Yu-- Good point about the cut-off. Maybe you're right and I don't want
> Lennard Jones for this. Also, can you tell me more about PLUMED?
> 
> Perhaps I made my question too convoluted. What I really want to know is
> how to manually add interactions between particular atom numbers of a
> single monomer. (The only caveat to this that might be important is that
> I'll want these interactions to end up applying to a number of monomers
> that will start far apart from each other.) Should I put them in [ pairs ],
> [ nonbonded_params ], or elsewhere? What happens to the parameters
> specified in [ atomtypes ] in each case? I'm worried that I'm changing the
> parameters in [ pairs ], while gromacs is never actually using those
> parameters, since maybe it thinks those should be 1-4 interactions (which
> they're not) or because it's using different sets of parameters instead or
> for some other reason.
> 
> Thanks again,
> Amanda
> 
> 
> 
> > ​Hello,
> >
> > I am trying to create my own topology file in order to simulate assembly
> of
> > a number of identical monomers. I have been reading the manual, mailing
> > list, and other online sources, about what all the sections in the
> topology
> > mean and how to construct them, but I'm still confused about what is
> > necessary and what overrides what.
> >
> > I would like to be able to have any number of monomers in my system and
> > therefore I want all the intermolecular interactions to be non-specific. I
> > want each monomer to have atom numbers running from 1 to last_atom_number,
> > so that I can have atom 1 paired with atom last_atom_number, and see
> > binding between any monomer's atom 1 with any other monomer's atom
> > last_atom_number.
> >
> > So my idea is to create a single topology file, which will contain the
> > intramolecular interactions for a single monomer, as well as the
> > interactions between atom 1 and atom last_atom_number. The latter will
> > probably be Lennard-Jones interactions, since that way the "beginning" of
> > one monomer will not interact with its own "end" (due to the cut-off), but
> > with other monomers' ends if they get close enough. I'd like to manually
> > adjust the parameters for these interactions, to accelerate binding.
> >
> > The problem is that I don't know where to put these Lennard Jones
> > interactions.
> >
> > Right now I have them in the [ pairs ] section, since my understanding is
> > that this is where one can put "extra" non-bonded interactions with
> special
> > parameters. But it also seems like this depends on the force field and
> that
> > sometimes [ pairs ] should only be for a list of 1-4 interactions. Since
> > I'm writing my own topology (not using pdb2gmx), what will [ pairs ]
> > specify? Will the parameters in [ pairs ] override the parameters in [
> > atomtypes ]? I have increased the c6 parameter and decreased the c12
> > parameter considerably, and I'm still not seeing any sign 

Re: [gmx-users] manually adding non-bonded interactions based on atom number to topology file

[Wes Barnett]

On Thu, Sep 28, 2017 at 1:10 PM, Amanda Parker  wrote:

> Hi again,
>
> For some reason I'm not getting your replies to my inbox, but I saw them in
> the Digest.
>
> Wes-- I would like to see a sort of phase transition, yes, in which a
> number of monomers go from a disordered to ordered state. The ordered state
> will look something like AB-AB-AB-... where AB represents a monomer that
> has an A end and a B end (using Yu's description) that are identical, and
> the "-" indicates an attractive interaction.
>
> Yu-- Good point about the cut-off. Maybe you're right and I don't want
> Lennard Jones for this. Also, can you tell me more about PLUMED?
>
> Perhaps I made my question too convoluted. What I really want to know is
> how to manually add interactions between particular atom numbers of a
> single monomer. (The only caveat to this that might be important is that
> I'll want these interactions to end up applying to a number of monomers
> that will start far apart from each other.) Should I put them in [ pairs ],
> [ nonbonded_params ], or elsewhere? What happens to the parameters
> specified in [ atomtypes ] in each case? I'm worried that I'm changing the
> parameters in [ pairs ], while gromacs is never actually using those
> parameters, since maybe it thinks those should be 1-4 interactions (which
> they're not) or because it's using different sets of parameters instead or
> for some other reason.
>
> Thanks again,
> Amanda
>

I'm still not quite getting what the system is. Are there bonds between
monomers? How many bonds are on each polymer? Have you been able to
simulate a regular polymer melt? What have you tried so far? My suggestion
is to start with a simpler system first and then work your way up to this
more complex system.

[ pairs ] is just for 1-4 non-bonded interactions. Do you want those in
your simulation? This all depends on what you have in [ defaults ] as well.
Do you have "gen-pairs" as yes? Are you excluding 1-4 non-bonded
interactions? Do you even have those in your system? From your description
above it looks like you have just two particles per molecule, so non-bonded
interactions between particles in the same molecule would be irrelevant.

[ nonbonded_params ] will override any previous combination rule. In this
section you must specify every interaction's parameters.

The simple answer to this question is - if you want different interactions
between different monomers, they need to be different atom types, and most
likely you'll want to specify each interaction in [ nonbonded_params ].

>
> 
>
> > ​Hello,
> >
> > I am trying to create my own topology file in order to simulate assembly
> of
> > a number of identical monomers. I have been reading the manual, mailing
> > list, and other online sources, about what all the sections in the
> topology
> > mean and how to construct them, but I'm still confused about what is
> > necessary and what overrides what.
> >
> > I would like to be able to have any number of monomers in my system and
> > therefore I want all the intermolecular interactions to be non-specific.
> I
> > want each monomer to have atom numbers running from 1 to
> last_atom_number,
> > so that I can have atom 1 paired with atom last_atom_number, and see
> > binding between any monomer's atom 1 with any other monomer's atom
> > last_atom_number.
> >
> > So my idea is to create a single topology file, which will contain the
> > intramolecular interactions for a single monomer, as well as the
> > interactions between atom 1 and atom last_atom_number. The latter will
> > probably be Lennard-Jones interactions, since that way the "beginning" of
> > one monomer will not interact with its own "end" (due to the cut-off),
> but
> > with other monomers' ends if they get close enough. I'd like to manually
> > adjust the parameters for these interactions, to accelerate binding.
> >
> > The problem is that I don't know where to put these Lennard Jones
> > interactions.
> >
> > Right now I have them in the [ pairs ] section, since my understanding is
> > that this is where one can put "extra" non-bonded interactions with
> special
> > parameters. But it also seems like this depends on the force field and
> that
> > sometimes [ pairs ] should only be for a list of 1-4 interactions. Since
> > I'm writing my own topology (not using pdb2gmx), what will [ pairs ]
> > specify? Will the parameters in [ pairs ] override the parameters in [
> > atomtypes ]? I have increased the c6 parameter and decreased the c12
> > parameter considerably, and I'm still not seeing any sign of attraction
> > between monomer-monomer interfaces.
> >
> > [ nonbonded_params ] actually seems like the right place, since I've read
> > that the parameters there *will* override the combination rules, but it
> > looks like this section doesn't take atom numbers, but only atom types.
> > Since I want these bonds to be based on site locations, this won't work.
> Is
> > 

Re: [gmx-users] manually adding non-bonded interactions based on atom number to topology file

[Amanda Parker]

Hi again,

For some reason I'm not getting your replies to my inbox, but I saw them in
the Digest.

Wes-- I would like to see a sort of phase transition, yes, in which a
number of monomers go from a disordered to ordered state. The ordered state
will look something like AB-AB-AB-... where AB represents a monomer that
has an A end and a B end (using Yu's description) that are identical, and
the "-" indicates an attractive interaction.

Yu-- Good point about the cut-off. Maybe you're right and I don't want
Lennard Jones for this. Also, can you tell me more about PLUMED?

Perhaps I made my question too convoluted. What I really want to know is
how to manually add interactions between particular atom numbers of a
single monomer. (The only caveat to this that might be important is that
I'll want these interactions to end up applying to a number of monomers
that will start far apart from each other.) Should I put them in [ pairs ],
[ nonbonded_params ], or elsewhere? What happens to the parameters
specified in [ atomtypes ] in each case? I'm worried that I'm changing the
parameters in [ pairs ], while gromacs is never actually using those
parameters, since maybe it thinks those should be 1-4 interactions (which
they're not) or because it's using different sets of parameters instead or
for some other reason.

Thanks again,
Amanda



> ​Hello,
>
> I am trying to create my own topology file in order to simulate assembly
of
> a number of identical monomers. I have been reading the manual, mailing
> list, and other online sources, about what all the sections in the
topology
> mean and how to construct them, but I'm still confused about what is
> necessary and what overrides what.
>
> I would like to be able to have any number of monomers in my system and
> therefore I want all the intermolecular interactions to be non-specific. I
> want each monomer to have atom numbers running from 1 to last_atom_number,
> so that I can have atom 1 paired with atom last_atom_number, and see
> binding between any monomer's atom 1 with any other monomer's atom
> last_atom_number.
>
> So my idea is to create a single topology file, which will contain the
> intramolecular interactions for a single monomer, as well as the
> interactions between atom 1 and atom last_atom_number. The latter will
> probably be Lennard-Jones interactions, since that way the "beginning" of
> one monomer will not interact with its own "end" (due to the cut-off), but
> with other monomers' ends if they get close enough. I'd like to manually
> adjust the parameters for these interactions, to accelerate binding.
>
> The problem is that I don't know where to put these Lennard Jones
> interactions.
>
> Right now I have them in the [ pairs ] section, since my understanding is
> that this is where one can put "extra" non-bonded interactions with
special
> parameters. But it also seems like this depends on the force field and
that
> sometimes [ pairs ] should only be for a list of 1-4 interactions. Since
> I'm writing my own topology (not using pdb2gmx), what will [ pairs ]
> specify? Will the parameters in [ pairs ] override the parameters in [
> atomtypes ]? I have increased the c6 parameter and decreased the c12
> parameter considerably, and I'm still not seeing any sign of attraction
> between monomer-monomer interfaces.
>
> [ nonbonded_params ] actually seems like the right place, since I've read
> that the parameters there *will* override the combination rules, but it
> looks like this section doesn't take atom numbers, but only atom types.
> Since I want these bonds to be based on site locations, this won't work.
Is
> there a way to specify non-bonded parameters using atom numbers?
>
> Any clarification you can provide will be helpful.
>

Before delving into this too much, to clarify: you want to simulate a
polymer melt with some modified interactions between the ends of each
polymer?

--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group 
Columbia University
w.barn...@columbia.edu
http://wbarnett.us



Hi,

First, You must need a very long simulation box because one monomer's
length exceed the cut-off.

I don't think only LJ can naturely make monomers linear polymer. I know you
need acceleration of one monomer's A end binding to the other's B end. So I
will recommend the PLUMED to add some far-large-near-small restraints
between A and B end of different monomers.

Cheers,
Yu
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Re: [gmx-users] p-coupling for inverted hexagonal phase

[Mohsen Ramezanpour]

I did this test already, actually. The main problem I am facing right now
is that the semi-isotropic test systems get equilibrated (judging on box
size for now) after ca. 50 ns or less.
BUT for the anisotropic coupling, the box sizes 1) fluctuate a lot and 2)
does not seem to be equilibrated even after 300 ns. This makes me less
confident on the results, especially with the point you mentioned on
the effect of anisotropic after a long simulation time.


Cheers,
Mohsen

On Thu, Sep 28, 2017 at 5:51 AM, Justin Lemkul  wrote:

>
>
> On 9/28/17 12:31 AM, Mohsen Ramezanpour wrote:
>
>> Thanks Justin for your comment,
>>
>> I think applying the semi-isotropic will put too much symmetry on the
>> system while it might not be the case and system should be free to change
>> if it is energetically favourable.
>> The semi-isotropic, in fact, is scaling both the X and Y sides of the
>> simulation box with the same factor, if I understood correctly. So, it
>> will
>> keep the original geometry of the system the same through the simulation
>> time.
>> Think of situations where the water channels prefer to be elongated in
>> either X or Y direction. This will prevent this, right?
>> Also, if there is any phase transition possible (e.g. from HII to
>> Lamellar), semi-isotropic will probably limit this transition more than
>> what an anisotropic coupling will do.
>>
>> Please let me know your thoughts on this.
>>
>
> It seems like you already have a rationale for what to do. In the absence
> of literature precedent, you should probably test both to confirm your
> suspicions and validate your approach. Just be aware of potential artifacts
> due to anisotropic pressure coupling. They can be quite extreme over the
> course of a long simulation.
>
> -Justin
>
>
> Cheers,
>> Mohsen
>>
>>
>> On Wed, Sep 27, 2017 at 6:26 PM, Justin Lemkul  wrote:
>>
>>
>>> On 9/27/17 10:57 AM, Mohsen Ramezanpour wrote:
>>>
>>> Hi Everyone,

 Please let me know your thoughts on this.


 I don't see why these would be anisotropic. The lateral dimension is
>>> symmetric, so it seems that semiisotropic would be most appropriate.
>>> Anisotropic pressure coupling can lead to significant distortions of the
>>> box, and is most applicable in crystalline systems.
>>>
>>> -Justin
>>>
>>> Thanks in advance,
>>>
 Cheers,
 Mohsen

 On Fri, Sep 22, 2017 at 11:13 AM, Mohsen Ramezanpour <
 ramezanpour.moh...@gmail.com> wrote:

 Dear Gromacs users,

> I am doing a simulation on inverted hexagonal (HII) phase composed of
> just
> lipids and water.
>
> (please have a look at HII phase here:
> https://openi.nlm.nih.gov/detailedresult.php?img=
> PMC2695813_1757-5036-2-3-3=4)
>
> My question is regarding the pressure coupling for such systems. I am
> using the anisotropic p-coupling at the moment:
>
> pcoupl = Parrinello-Rahman; replaced
> pcoupltype  = anisotropic
> tau_p  = 5.0
> compressibility   = 4.5e-5  4.5e-5  4.5e-5  0 0 0
> ref_p   = 1.0 1.0 1.0 0 0 0
>
> I think this is the correct way to treat this type of system.
>
> Some might argue that a semi-isotropic p-coupling is the correct
> treatment for that. i.e.
>
> pcoupl = Parrinello-Rahman; replaced
> pcoupltype  = anisotropic
> tau_p  = 5.0
> compressibility   = 4.5e-5  4.5e-5
> ref_p   = 1.0 1.0
>
> where the first is for Z (the cylindrical axis of HII phase) and the
> second parameters control and scale the box size in both X and Y
> directions
> equally.
>
> I just like to know your opinions on this. Which one do you think is
> the
> better way to treat such systems?
>
> Thanks in advance for your comments.
> Mohsen
>
>
>
> --
> *Rewards work better than punishment ...*
>
>
>

 --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>> --
>>> 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.
> Assistant Professor
> Virginia 

Re: [gmx-users] distance/bonds restrains in gromacs2016.3 with domain decomposition

[Justin Lemkul]

On 9/28/17 2:11 AM, Yulian Gavrilov wrote:

No, at this point I am not applying any special conditions.


The full section of the .log file pertaining to DD setup would be useful 
here. We're just seeing the last bit, but how mdrun constructs the DD 
cells based on topological information often provides clues.


-Justin


On 28 September 2017 at 03:23, Justin Lemkul  wrote:



On 9/25/17 6:57 AM, Yulian Gavrilov wrote:


Dear all,

I try to restrain the conformation of a protein using distance/bonds
restrains.
I have a problem when I try to use distance restraints or restraint
potential (bonds type 10) together with domain decomposition.

I use gromacs2016.3. It seems that this issue should be solved for 2016
version:
http://manual.gromacs.org/documentation/2016.1/ReleaseNotes/
release-notes.html
[Made distance restraints work with threads and DD]

However, I get an error (both for bonds and distance restraints):

Fatal error:
There is no domain decomposition for 8 ranks that is compatible with the
given
box and a minimum cell size of 9.15291 nm
Change the number of ranks or mdrun option -rdd or -dds [this does not
help]
Look in the log file for details on the domain decomposition



My steps:

1. Add to .top file:

[ bonds ]
; ai   aj   typelow up1 up2 kdr
43   87 100.28 0.310.33 1000
53  107 100.28 0.310.33 1000
...

or

[ distance_restraints ]
; ai   aj   type   index   type'  low up1 up2 fac
43   87  1   0   1  0.280.310.331.0
53  107  1   0   1  0.280.310.331.0
...

in case of  [ distance_restraints ] I add to mdp file:
disre   = simple; simple or ensemble
;nstdisreout=0
disre-fc= 1000; [kJ mol^-1 nm^-2]

2. Run it with this script:

#PBS -q sleep -l select=8:ncpus=8:mem=5000mb
...
echo Using modules `module list`
setenv OMP_NUM_THREADS 8
...
module load mkl/11.3.4.258  gcc/4.9.3  impi/5.1.3.258
source /usr/local/gromacs-2016.3/bin/GMXRC.csh
...
mpirun gmx_mpi mdrun -v -deffnm md100ns


Please can you suggest something or explain what I am doing wrong?



A minimum DD cell size of 9 nm seems unrelated to distance restraints of
0.3 nm. Are you applying any other strange conditions? Free energy code or
custom exclusions?

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] p-coupling for inverted hexagonal phase

[Justin Lemkul]

On 9/28/17 12:31 AM, Mohsen Ramezanpour wrote:

Thanks Justin for your comment,

I think applying the semi-isotropic will put too much symmetry on the
system while it might not be the case and system should be free to change
if it is energetically favourable.
The semi-isotropic, in fact, is scaling both the X and Y sides of the
simulation box with the same factor, if I understood correctly. So, it will
keep the original geometry of the system the same through the simulation
time.
Think of situations where the water channels prefer to be elongated in
either X or Y direction. This will prevent this, right?
Also, if there is any phase transition possible (e.g. from HII to
Lamellar), semi-isotropic will probably limit this transition more than
what an anisotropic coupling will do.

Please let me know your thoughts on this.


It seems like you already have a rationale for what to do. In the 
absence of literature precedent, you should probably test both to 
confirm your suspicions and validate your approach. Just be aware of 
potential artifacts due to anisotropic pressure coupling. They can be 
quite extreme over the course of a long simulation.


-Justin


Cheers,
Mohsen


On Wed, Sep 27, 2017 at 6:26 PM, Justin Lemkul  wrote:



On 9/27/17 10:57 AM, Mohsen Ramezanpour wrote:


Hi Everyone,

Please let me know your thoughts on this.



I don't see why these would be anisotropic. The lateral dimension is
symmetric, so it seems that semiisotropic would be most appropriate.
Anisotropic pressure coupling can lead to significant distortions of the
box, and is most applicable in crystalline systems.

-Justin

Thanks in advance,

Cheers,
Mohsen

On Fri, Sep 22, 2017 at 11:13 AM, Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

Dear Gromacs users,

I am doing a simulation on inverted hexagonal (HII) phase composed of
just
lipids and water.

(please have a look at HII phase here:
https://openi.nlm.nih.gov/detailedresult.php?img=
PMC2695813_1757-5036-2-3-3=4)

My question is regarding the pressure coupling for such systems. I am
using the anisotropic p-coupling at the moment:

pcoupl = Parrinello-Rahman; replaced
pcoupltype  = anisotropic
tau_p  = 5.0
compressibility   = 4.5e-5  4.5e-5  4.5e-5  0 0 0
ref_p   = 1.0 1.0 1.0 0 0 0

I think this is the correct way to treat this type of system.

Some might argue that a semi-isotropic p-coupling is the correct
treatment for that. i.e.

pcoupl = Parrinello-Rahman; replaced
pcoupltype  = anisotropic
tau_p  = 5.0
compressibility   = 4.5e-5  4.5e-5
ref_p   = 1.0 1.0

where the first is for Z (the cylindrical axis of HII phase) and the
second parameters control and scale the box size in both X and Y
directions
equally.

I just like to know your opinions on this. Which one do you think is the
better way to treat such systems?

Thanks in advance for your comments.
Mohsen



--
*Rewards work better than punishment ...*






--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] grompp very slow generating .tpr when excluded bonded neighbours is large

[Justin Lemkul]

On 9/28/17 12:25 AM, Dallas Warren wrote:

Justin,

No, I have separate index groups for each of the atom types.

Wouldn't that still have the pair of atoms that are located on the
same molecule, contributing to the RDF?

Molecule is like this:
C1 ---C38

Index file would be something like this:
[ C1 ]
1 39 77 .

[ C38 ]
38 76 114 

So doesn't it still include these atom pairs to generate the RDF? Atom
pair list below.  From the RDFs that are generating using this method,
it appears it does as there is a massive peak around the intra-atomic
distance.

1-38, 1-76, 1-114 . 39-38, 39-76, 39-114 

First and fifth pair in this list are atoms that are contained within
the same molecule.

Wouldn't be surprised if I am missing something simple here .


No, I misunderstood what you were actually after. What you are asking 
for does require a huge intramolecular nrexcl and you are indeed 
seemingly running out of memory trying to create such a huge exclusion 
list. Sorry to say I don't have much more to suggest here.


-Justin


Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 28 September 2017 at 10:27, Justin Lemkul  wrote:


On 9/27/17 7:54 PM, Dallas Warren wrote:

Left the 37 one running, and it ended up being "Killed". Was
distracted, so didn't really see how long it ran etc, but suspect it
was due to amount of memory being used up.

I am going about this the right way? i.e. want the RDF between atoms
at either end of the molecule (38 atoms long), and don't want the
atoms within the same molecule included in the calculation then need
to set nrexcl to 37?


I'm assuming you're trying to get the RDF simply by selecting the whole
molecule? Why not just use index groups with the starting and ending atoms
in separate groups and compute the RDF of one around the other?

-Justin



Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On 28 September 2017 at 09:02, Dallas Warren 
wrote:

Just want to check that this should be taking as long as it is
(expected behaviour etc), for grompp to generate the tpr when nrexcl
is large.

I have a long straight chain molecule with 38 atoms that are
generating RDFs for, so need to change the [ moleculetype ] nrexcl to
exclude atoms within the same molecule from the generated RDFs.
Initially set nrexcl to 37, ran grompp to get the tpr, and it was
taking a lng time and consuming significant amounts of memory.
Killed it and ran a few tests with increasing values and it is pretty
much instantaneous up until about 25.  Each increase after that
increases the time it takes in the " excluding ## bonded neighbours
molecule type '' " step.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] protein ligand faraway from one another

[Du, Yu]

> -Original Messages-
> From: "Fakhar Alam" 
> Sent Time: 2017-09-28 16:07:52 (Thursday)
> To: gmx-us...@gromacs.org
> Cc: 
> Subject: [gmx-users] protein ligand faraway from one another
> 
> Dear Gromacs Experts,
> 
> I am doing simulation of protein-ligand complex. However when I follow the
> steps in the tutorial, the ligand is very faraway from the protein. How can
> I put the ligand close to the protein ?
> 
> Thanks,
> Alam
> -- 
> Gromacs Users mailing list
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Before simulation, the protein and ligand is a complex, right?

Can you give the detail of which tutorial you are following and which step have 
you followed to?
Do you follow the tutorial exactly or tune some factors that can impact the 
interaction between protein and ligand?
I have never encountered the problem. We need more information to answer your 
question.

--
Yu
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[gmx-users] protein ligand faraway from one another

[Fakhar Alam]

Dear Gromacs Experts,

I am doing simulation of protein-ligand complex. However when I follow the
steps in the tutorial, the ligand is very faraway from the protein. How can
I put the ligand close to the protein ?

Thanks,
Alam
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Re: [gmx-users] distance/bonds restrains in gromacs2016.3 with domain decomposition

[Yulian Gavrilov]

No, at this point I am not applying any special conditions.

On 28 September 2017 at 03:23, Justin Lemkul  wrote:

>
>
> On 9/25/17 6:57 AM, Yulian Gavrilov wrote:
>
>> Dear all,
>>
>> I try to restrain the conformation of a protein using distance/bonds
>> restrains.
>> I have a problem when I try to use distance restraints or restraint
>> potential (bonds type 10) together with domain decomposition.
>>
>> I use gromacs2016.3. It seems that this issue should be solved for 2016
>> version:
>> http://manual.gromacs.org/documentation/2016.1/ReleaseNotes/
>> release-notes.html
>> [Made distance restraints work with threads and DD]
>>
>> However, I get an error (both for bonds and distance restraints):
>>
>> Fatal error:
>> There is no domain decomposition for 8 ranks that is compatible with the
>> given
>> box and a minimum cell size of 9.15291 nm
>> Change the number of ranks or mdrun option -rdd or -dds [this does not
>> help]
>> Look in the log file for details on the domain decomposition
>>
>>
>>
>> My steps:
>>
>> 1. Add to .top file:
>>
>> [ bonds ]
>> ; ai   aj   typelow up1 up2 kdr
>>43   87 100.28 0.310.33 1000
>>53  107 100.28 0.310.33 1000
>> ...
>>
>> or
>>
>> [ distance_restraints ]
>> ; ai   aj   type   index   type'  low up1 up2 fac
>>43   87  1   0   1  0.280.310.331.0
>>53  107  1   0   1  0.280.310.331.0
>> ...
>>
>> in case of  [ distance_restraints ] I add to mdp file:
>> disre   = simple; simple or ensemble
>> ;nstdisreout=0
>> disre-fc= 1000; [kJ mol^-1 nm^-2]
>>
>> 2. Run it with this script:
>>
>> #PBS -q sleep -l select=8:ncpus=8:mem=5000mb
>> ...
>> echo Using modules `module list`
>> setenv OMP_NUM_THREADS 8
>> ...
>> module load mkl/11.3.4.258  gcc/4.9.3  impi/5.1.3.258
>> source /usr/local/gromacs-2016.3/bin/GMXRC.csh
>> ...
>> mpirun gmx_mpi mdrun -v -deffnm md100ns
>>
>>
>> Please can you suggest something or explain what I am doing wrong?
>>
>>
> A minimum DD cell size of 9 nm seems unrelated to distance restraints of
> 0.3 nm. Are you applying any other strange conditions? Free energy code or
> custom exclusions?
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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>



-- 
Sincerely,
Yulian Gavrilov
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