Re: [gmx-users] GMX-PLUMED speed

[XAvier Periole]

They have a forum! I do agree it is more appropriate there! 

Tks,
X-

> On 05 Feb 2017, at 17:19, Justin Lemkul  wrote:
> 
> 
> 
> On 2/5/17 3:49 AM, XAvier Periole wrote:
>> 
>> Dears,
>> 
>> I am using gromacs v5.1.4 with PLUMED v2.3.0.
>> 
>> Through my experience as a novice in using PLUMED, I have noticed that not 
>> writing the restraint/forces info in a file and not using a STRIDE 
>> accelerate the code significantly.
>> 
>> Using a line such as follows in the plumed parameters set:
>> PRINT ARG=restraint.bias
>> 
>> instead of the most correct:
>> PRINT STRIDE=1 ARG=restraint.bias FILE=bias
>> 
>> would make gmx run at 950 ns/day instead of 550 ns/day.
>> 
>> The inconvenient is that the log file becomes large (all the restraint are 
>> written in it) and messy (the values are mixing with the rest of the info on 
>> exchanges), but the speed up is considerable.
>> 
>> Note that I still print the values of the restraint in a file, which I 
>> haven’t tried to remove but it could also speed up the run.
>> 
>> Someone should may be look at this as he speed up applies on XX replicas so 
>> lots of CPU time (cooling system, energy, climat change, …) is wasted.
>> 
> 
> Have you reported this to the PLUMED forum?  They'll certainly want to know 
> (and it's probably more applicable there, anyway).
> 
> -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 <mailto:jalem...@outerbanks.umaryland.edu> 
> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul 
> <http://mackerell.umaryland.edu/~jalemkul>
> 
> ==
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[gmx-users] GMX-PLUMED speed

[XAvier Periole]

Dears,

I am using gromacs v5.1.4 with PLUMED v2.3.0.

Through my experience as a novice in using PLUMED, I have noticed that not 
writing the restraint/forces info in a file and not using a STRIDE accelerate 
the code significantly. 

Using a line such as follows in the plumed parameters set:
PRINT ARG=restraint.bias

instead of the most correct:
PRINT STRIDE=1 ARG=restraint.bias FILE=bias 

would make gmx run at 950 ns/day instead of 550 ns/day. 

The inconvenient is that the log file becomes large (all the restraint are 
written in it) and messy (the values are mixing with the rest of the info on 
exchanges), but the speed up is considerable. 
 
Note that I still print the values of the restraint in a file, which I haven’t 
tried to remove but it could also speed up the run.

Someone should may be look at this as he speed up applies on XX replicas so 
lots of CPU time (cooling system, energy, climat change, …) is wasted. 

I hope this helps.
X-
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Re: [gmx-users] how to arbitrarily increase the XY size of an existing bilayer system (adding more lipids)

[XAvier Periole]

Indeed same Thomas has good points I could have mentioned. 

Reduce the interface gap to a minimum of the system ca get stuck in stupid 
state … the two side should see each other, once they start merging it is fast. 

XAvier.

> On 01 Feb 2017, at 20:01, Thomas Piggot  wrote:
> 
> I've actually used this suggested approach before (when making a larger 
> membrane smaller). It can take a fair bit of simulation to equilibrate things 
> at the periodic boundary, depending upon how you remove the lipids, how big 
> you make the box at the boundary, etc. Not making the interface big enough, 
> so as to try and make the gap between periodic images small for a quick 
> equilibration, can easily lead to crashes due to overlapping atoms across the 
> periodic boundary.
> 
> What lipids and force field you are using will also massively impact the 
> equilibration times. For a fast diffusing phospholipid (using a fast 
> diffusing force field and cut-off settings), taking your original suggestion 
> a), or the approach of Xavier may make the equilibration quick enough that 
> it's not worth the effort of doing something more elaborate.
> 
> Cheers
> 
> Tom
> 
> On 01/02/17 17:30, Christopher Neale wrote:
>> Another great idea. Thanks Xavier! I'll report back on what I eventually do 
>> in a few weeks with info on issues and timescales necessary for relaxation 
>> so that it's available if anyone ever wants to do it in the future.
>> ____________
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>>  on behalf of XAvier 
>> Periole 
>> Sent: 01 February 2017 11:18:36
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] how to arbitrarily increase the XY size of an  
>> existing bilayer system (adding more lipids)
>> 
>> What about tilling 2x2 and then removing lipids that have x&y larger than a 
>> cutoff … then minimisation+equilibration of the interface even atomistic 
>> would be quite trivial.
>> 
>> X-
>> 
>>> On 01 Feb 2017, at 17:14, Christopher Neale  
>>> wrote:
>>> 
>>> Dear Users:
>>> 
>>> I have some atomistic systems of a membrane protein embedded in a lipid 
>>> bilayer. I currently have N lipids and I would like to increase that to 
>>> 1.5N or 2N lipids (distributed equally in the bilayer plane) without 
>>> disturbing the existing structure. Increasing to 4N lipids would be 
>>> relatively easy by tiling the exisintg lipids 2x2 in XY. I am writing to 
>>> ask if anybody has ever done this and if they have any suggestions.
>>> 
>>> The ideas that I have at present are:
>>> a) add lipids and equilibrate (using restaints on existing lipids and 
>>> protein). Increase in size could be by simply increasing XY dimensions and 
>>> then using gmx genbox, knowing that I will end up with a bilayer defect at 
>>> the edges that I will have to heal by MD.
>>> b) convert to a CG model, add lipids and equilibrate, then back to an AA 
>>> model (using restaints on existing lipids and protein)
>>> 
>>> I realize it sounds like an absurd requirement, but for scientific reasons 
>>> in this particular case I can not simply start over by embedding the 
>>> protein in a new, larger bilayer (i.e., it’s not just about saving compute 
>>> time when generating the larger systems).
>>> 
>>> Thank you for any advice,
>>> Chris.
>>> --
>>> Gromacs Users mailing list
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> 
> -- 
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> Visiting Fellow
> University of Southampton, UK.
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Re: [gmx-users] how to arbitrarily increase the XY size of an existing bilayer system (adding more lipids)

[XAvier Periole]

What about tilling 2x2 and then removing lipids that have x&y larger than a 
cutoff … then minimisation+equilibration of the interface even atomistic would 
be quite trivial.

X-

> On 01 Feb 2017, at 17:14, Christopher Neale  
> wrote:
> 
> Dear Users:
> 
> I have some atomistic systems of a membrane protein embedded in a lipid 
> bilayer. I currently have N lipids and I would like to increase that to 1.5N 
> or 2N lipids (distributed equally in the bilayer plane) without disturbing 
> the existing structure. Increasing to 4N lipids would be relatively easy by 
> tiling the exisintg lipids 2x2 in XY. I am writing to ask if anybody has ever 
> done this and if they have any suggestions.
> 
> The ideas that I have at present are:
> a) add lipids and equilibrate (using restaints on existing lipids and 
> protein). Increase in size could be by simply increasing XY dimensions and 
> then using gmx genbox, knowing that I will end up with a bilayer defect at 
> the edges that I will have to heal by MD.
> b) convert to a CG model, add lipids and equilibrate, then back to an AA 
> model (using restaints on existing lipids and protein)
> 
> I realize it sounds like an absurd requirement, but for scientific reasons in 
> this particular case I can not simply start over by embedding the protein in 
> a new, larger bilayer (i.e., it’s not just about saving compute time when 
> generating the larger systems).
> 
> Thank you for any advice,
> Chris.
> -- 
> Gromacs Users mailing list
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Re: [gmx-users] Inverse CG MARTINI trajectory

[XAvier Periole]

There is an older tool than backward accessible on cgmartini.nl 
, it is in the reverse section … works with an older 
version of gmx.

I believe other people have developed similar tools but not sure that they work 
on xtc.

But I’d be suggesting you try to contact Tsjerk on the Martini Blog. It is 
always good to report errors and get them fixed.

XA-

> On 28 Jul 2016, at 16:44, shivangi nangia  wrote:
> 
> Dear Gromacs Users,
> 
> I need to inverse CG a MARTINI trajecory.
> 
> 
> I have been using the Backward script successfully multiple times with gro
> files.
> 
> However, this time I need .xtc as the inverse coarse grained output
> trajectory.
> 
> I tried backward script but it runs into an error.
> 
> Is there any other tool or utility that will inverse CG a MARTINI .xtc to
> all-atom .xtc.?
> 
> Many thanks in advance,
> sxn
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[gmx-users] trouble using tables with 5.1

[XAvier Periole]

Dears,
Note: At the end of the message I provide a solution found while writing the 
email ...

I am having troubles feeding mdrun my tabulated bonded terms through tables. 
The manual does not indicate any change in that respect … 

I used to run this with gmx-463 with the command looking like:
mdrun  -tableb /path/table 

my tabulated potentials being named:
table_a0.xvg table_a1.xvg 
table_d0.xvg … table_d13.xvg 

With the same syntax (-tableb table) using gmx5.1 I get the following error 
message:
-
Error in user input:
Invalid common-line options 
  In command-line option -tableb
File ‘table’ does not exist or is not accessible.
The following extensions were tried to complete the file name

if I add .xvg to the name table (-tableb table.xvg) I get the error:

Error in user input:
Invalid common-line options 
  In command-line option -tableb
File ‘table’ does not exist or is not accessible.

if I give the fill name of one table (-table table_a0.xvg) I get the error:
——
System I/O error:
Library file ‘table_a0_a0.xvg’ not found in the current directory no in the 
default directories.
The following path …

Solution: then is I give the name table.xvg (-tableb table.xvg) and create an 
empty file then it all goes smooth and the files are red and mdrun … 

Beautiful, but might be some funky stuff happening that could be fixed. 

Tks,
XAvier.
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Re: [gmx-users] Using ATB to generate valid topologies

[XAvier Periole]

Tks for the references. 

For the record, here are the references for ATB:
DOI: 10.1021/ct200196m <http://pubs.acs.org/doi/abs/10.1021/ct200196m>
DOI:10.1089/cmb.2012.0239 <http://dx.doi.org/10.1089/cmb.2012.0239>
DOI:10.1007/s10822-014-9713-7 <http://dx.doi.org/10.1007/s10822-014-9713-7>

X-

> On 13 Jul 2016, at 17:39, Justin Lemkul  wrote:
> 
> 
> 
> On 7/13/16 11:02 AM, XAvier Periole wrote:
>>>> 
>>>> Just for the record ATB is a very good tool to build a start up topology. 
>>>> They also have a large set of topologies available on the site.
>>>> 
>>>> The charges are determined by QM and the user chooses the level of 
>>>> accuracy.
>>>> The bonded and LJ parameters are chosen based on the type of atom and it 
>>>> connectivity. Most atom types are already existing.
>>>> 
>>>> The sad part of ATB and other automated topology builders is that it is 
>>>> difficult to make a correct topology without putting the hands in.
>>>> 
>>>> Note that the CHARMM topology builder is even worst that ATB, but it gives 
>>>> you consistent topologies with existing ones.
>>>> 
>>> 
>>> Which CHARMM topology builder?  CGenFF or ParamChem?  I'd be curious to 
>>> know the basis upon which this claim is made.
>> My experience in building CHARMM topologies … building from existing 
>> topologies is rather coarse!
>>> CHARMM and GROMOS follow very different parametrization protocols, so if a 
>>> systematic analysis has been done, in the context of the relative accuracy 
>>> of the parent force fields, I would really like to see the results.  I 
>>> think that would be a very valuable effort.
>> Yes CGgenFF, it builds from building blocks and not clear to me how it 
>> adjusts the charges … but no QM!
>>> 
>>> Note that at least CGenFF gives penalty scores for all parameters that it 
>>> provides the user, specifically telling which parameters will require 
>>> additional work.
>> How does it determine them?
>> No penalty does not guaranty good parameters but small expected deviation 
>> from existing topology …
>>> 
> 
> The answers to your questions above are published (particularly the second 
> paper):
> 
> http://dx.doi.org/10.1021/ci300363c <http://dx.doi.org/10.1021/ci300363c>
> http://dx.doi.org/10.1021/ci3003649 <http://dx.doi.org/10.1021/ci3003649>
> 
> -Justin
> 
>>>> In short: You need an experienced modeller to help you “validating” your 
>>>> topology.
>>>> 
>>> 
>>> Agreed 100%.  There is no black box method that is perfect or can be 
>>> trusted implicitly.  Some are better than others, but force fields are as 
>>> much an art as they are a science.  A perfect, hands-off method for 
>>> parametrization of any molecule is, at present, untenable.
>>> 
>>> -Justin
>>> 
>>>> X-
>>>> 
>>>>> On 12 Jul 2016, at 14:40, David van der Spoel  
>>>>> wrote:
>>>>> 
>>>>> On 12/07/16 13:47, Justin Lemkul wrote:
>>>>>> 
>>>>>> 
>>>>>> On 7/11/16 9:52 AM, ALEXANDER DHALIWAL wrote:
>>>>>>> Dear GROMACS users,
>>>>>>> 
>>>>>>> I am pioneering the use of GROMACS in my lab to supplement some of our
>>>>>>> experimental research. I have generated some topologies from the
>>>>>>> Automated
>>>>>>> Topology Builder (ATB), but I am unsure whether or not to trust the 
>>>>>>> files
>>>>>>> provided by this service. I am only an undergrad, so I would not feel
>>>>>>> comfortable asking my supervisor to invest thousands of dollars into a
>>>>>>> program such as Gaussian09 to validate these topologies. Does this
>>>>>> 
>>>>>> One would not use Gaussian to validate ATB topologies.  One would
>>>>>> generally *start* with a QM calculation to get charge distributions,
>>>>>> then validate against other data.  The problem with the GROMOS force
>>>>>> field is that there is little connection between QM calculations and the
>>>>>> final topologies.  I have posted at length on this topic just within the
>>>>>> last few days; please check the archive.
>>>>>> 
>>>>>>> community trust the outputs of ATB and, if not, could you pr

Re: [gmx-users] Using ATB to generate valid topologies

[XAvier Periole]

>> 
>> Just for the record ATB is a very good tool to build a start up topology. 
>> They also have a large set of topologies available on the site.
>> 
>> The charges are determined by QM and the user chooses the level of accuracy.
>> The bonded and LJ parameters are chosen based on the type of atom and it 
>> connectivity. Most atom types are already existing.
>> 
>> The sad part of ATB and other automated topology builders is that it is 
>> difficult to make a correct topology without putting the hands in.
>> 
>> Note that the CHARMM topology builder is even worst that ATB, but it gives 
>> you consistent topologies with existing ones.
>> 
> 
> Which CHARMM topology builder?  CGenFF or ParamChem?  I'd be curious to know 
> the basis upon which this claim is made.  
My experience in building CHARMM topologies … building from existing topologies 
is rather coarse! 
> CHARMM and GROMOS follow very different parametrization protocols, so if a 
> systematic analysis has been done, in the context of the relative accuracy of 
> the parent force fields, I would really like to see the results.  I think 
> that would be a very valuable effort.
Yes CGgenFF, it builds from building blocks and not clear to me how it adjusts 
the charges … but no QM!
> 
> Note that at least CGenFF gives penalty scores for all parameters that it 
> provides the user, specifically telling which parameters will require 
> additional work.
How does it determine them? 
No penalty does not guaranty good parameters but small expected deviation from 
existing topology … 
> 
>> In short: You need an experienced modeller to help you “validating” your 
>> topology.
>> 
> 
> Agreed 100%.  There is no black box method that is perfect or can be trusted 
> implicitly.  Some are better than others, but force fields are as much an art 
> as they are a science.  A perfect, hands-off method for parametrization of 
> any molecule is, at present, untenable.
> 
> -Justin
> 
>> X-
>> 
>>> On 12 Jul 2016, at 14:40, David van der Spoel  wrote:
>>> 
>>> On 12/07/16 13:47, Justin Lemkul wrote:
 
 
 On 7/11/16 9:52 AM, ALEXANDER DHALIWAL wrote:
> Dear GROMACS users,
> 
> I am pioneering the use of GROMACS in my lab to supplement some of our
> experimental research. I have generated some topologies from the
> Automated
> Topology Builder (ATB), but I am unsure whether or not to trust the files
> provided by this service. I am only an undergrad, so I would not feel
> comfortable asking my supervisor to invest thousands of dollars into a
> program such as Gaussian09 to validate these topologies. Does this
 
 One would not use Gaussian to validate ATB topologies.  One would
 generally *start* with a QM calculation to get charge distributions,
 then validate against other data.  The problem with the GROMOS force
 field is that there is little connection between QM calculations and the
 final topologies.  I have posted at length on this topic just within the
 last few days; please check the archive.
 
> community trust the outputs of ATB and, if not, could you provide me with
> suggestions as to how I may validate my topologies given my
> restraints? Any
> advice would be much appreciated.
> 
 
 It depends on how complex the molecules are.  GROMOS parametrization is
 empirical; existing building blocks are put together to yield a
 molecule, and any unknown groups or strange linkages are explicitly
 parametrized using model compounds.  I don't recall all the guts of what
 ATB does (I haven't used the GROMOS force field in a long time) but I
 believe it is doing this, coupled with a quick QM calculation for charge
 refinement in the case that the constituent groups are not easily looked
 up from an existing database).  In general, the topologies from ATB are
 significantly better than from, e.g. PRODRG, but the skeptic/force field
 purist in me never trusts a black box.  The problem, when it comes to
 ligands/drugs is lack of target data.  For small molecules, there are
 thermodynamic properties that one can look at.  For more complex things
 like drugs, you might get lucky and have something like a logP tabulated
 somewhere, but such data can often be difficult or impossible to obtain.
 
 -Justin
 
>>> http://virtualchemistry.org provides validated topologies for about 150 
>>> compounds, that is force fields have been tested by running liquid 
>>> simulations.
>>> 
>>> 
>>> --
>>> 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
>>> --
>>> 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.o

Re: [gmx-users] Using ATB to generate valid topologies

[XAvier Periole]

Just for the record ATB is a very good tool to build a start up topology. They 
also have a large set of topologies available on the site. 

The charges are determined by QM and the user chooses the level of accuracy. 
The bonded and LJ parameters are chosen based on the type of atom and it 
connectivity. Most atom types are already existing.

The sad part of ATB and other automated topology builders is that it is 
difficult to make a correct topology without putting the hands in. 

Note that the CHARMM topology builder is even worst that ATB, but it gives you 
consistent topologies with existing ones.

In short: You need an experienced modeller to help you “validating” your 
topology. 

X-

> On 12 Jul 2016, at 14:40, David van der Spoel  wrote:
> 
> On 12/07/16 13:47, Justin Lemkul wrote:
>> 
>> 
>> On 7/11/16 9:52 AM, ALEXANDER DHALIWAL wrote:
>>> Dear GROMACS users,
>>> 
>>> I am pioneering the use of GROMACS in my lab to supplement some of our
>>> experimental research. I have generated some topologies from the
>>> Automated
>>> Topology Builder (ATB), but I am unsure whether or not to trust the files
>>> provided by this service. I am only an undergrad, so I would not feel
>>> comfortable asking my supervisor to invest thousands of dollars into a
>>> program such as Gaussian09 to validate these topologies. Does this
>> 
>> One would not use Gaussian to validate ATB topologies.  One would
>> generally *start* with a QM calculation to get charge distributions,
>> then validate against other data.  The problem with the GROMOS force
>> field is that there is little connection between QM calculations and the
>> final topologies.  I have posted at length on this topic just within the
>> last few days; please check the archive.
>> 
>>> community trust the outputs of ATB and, if not, could you provide me with
>>> suggestions as to how I may validate my topologies given my
>>> restraints? Any
>>> advice would be much appreciated.
>>> 
>> 
>> It depends on how complex the molecules are.  GROMOS parametrization is
>> empirical; existing building blocks are put together to yield a
>> molecule, and any unknown groups or strange linkages are explicitly
>> parametrized using model compounds.  I don't recall all the guts of what
>> ATB does (I haven't used the GROMOS force field in a long time) but I
>> believe it is doing this, coupled with a quick QM calculation for charge
>> refinement in the case that the constituent groups are not easily looked
>> up from an existing database).  In general, the topologies from ATB are
>> significantly better than from, e.g. PRODRG, but the skeptic/force field
>> purist in me never trusts a black box.  The problem, when it comes to
>> ligands/drugs is lack of target data.  For small molecules, there are
>> thermodynamic properties that one can look at.  For more complex things
>> like drugs, you might get lucky and have something like a logP tabulated
>> somewhere, but such data can often be difficult or impossible to obtain.
>> 
>> -Justin
>> 
> http://virtualchemistry.org provides validated topologies for about 150 
> compounds, that is force fields have been tested by running liquid 
> simulations.
> 
> 
> -- 
> 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
> -- 
> Gromacs Users mailing list
> 
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Re: [gmx-users] [pairs] vs [exclusions]

[XAvier Periole]

Hi Peter,

Wouldn’t the exclusion act on the regular LJ and pairs add a different LJ(14)? 

With exclusions, do you have the regular LJ present?

XAvier.

> On 13 Jul 2016, at 13:17, Peter Kroon  wrote:
> 
> Hi Mark (and list),
> 
> thanks for the ideas.
> `gmx check -s1 with_excl.tpr -s2 no_excl.tpr` didn't tell me much,
> unfortunately:
> ...
> comparing blocka excls
> excls.nra (1944 - 1920)
> comparing groups
> ...
> 
> I think this means that with_excl.tpr contains 22 more exclusions.
> 
> Running gmx dump on both files shows that both list the relevant `LJC-14
> q` entries. However, with_excl.tpr also produces the appropriate exclusions.
> 
> So which takes precedence? From these results I'm tempted to think the
> exclusions take precedence, otherwise they wouldn't end up in the tpr.
> Or does mdrun do something intelligent here?
> 
> Peter
> 
> 
> On 13/07/16 12:18, Mark Abraham wrote:
>> Hi,
>> 
>> I don't know which acts first, but making a few such .tpr files and
>> (hopefully) gmx check on them should make clear what happens. Or worst case
>> gmx dump the .tpr and do a textual diff. You can probably make your life
>> easier by playing around with atoms with high indices.
>> 
>> Mark
>> 
>> On Wed, Jul 13, 2016 at 10:46 AM Peter Kroon  wrote:
>> 
>>> Dear list,
>>> 
>>> I a have a short question on topologies, and the manual is somewhat
>>> unclear.
>>> If I have a topology which defines both an exclusion between an atom
>>> pair and a specific interaction between them using the [pairs] directive
>>> (function type 2), will they then have a non-bonded interaction, or not?
>>> 
>>> Thanks in advance,
>>> Peter Kroon
>>> 
>>> PS.
>>> short example topology:
>>> 
>>> [ moleculetype ]
>>> my_molecule 1
>>> 
>>> [ atoms ]
>>> ...
>>> 
>>> [ pairs ]
>>> 1   4   2   .
>>> 
>>> [ exclusions ]
>>> 1   4
>>> 
>>> [ bonds ]
>>> no bond between 1 and 4
>>> 
>>> ...
>>> 
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Re: [gmx-users] elastic restraints in MARTINI simulation

[Xavier Periole]

Any reference to illustrate the unphysical behavior of macromolecular systems 
using Berendsen thermostat compare to others?

XAvier. 

> On Mar 23, 2016, at 10:42, James Starlight  wrote:
> 
> Btw taking back to my question regarding thermostats in CG sims- does
> the correct choise influence on sampling here`? E.g in full atomistic
> sims generally langevens dynamics produces better results in
> comparison to berendsen thermostat which produce very unphysical
> behaviour for the macromolecular systems.
> 
> J.
> 
> 2016-03-23 10:32 GMT+01:00 Tsjerk Wassenaar :
>> Hi Mark,
>> 
>> In combination with the time step and maybe the particle mass, that would
>> be lovely. A dynamic update, based on the actual displacements would also
>> be possible after some steps (-rdd -1 ?).
>> 
>> Cheers,
>> 
>> Tsjerk
>>> On Mar 23, 2016 09:37, "Mark Abraham"  wrote:
>>> 
>>> Hi,
>>> 
>>> Tsjerk, does it make sense to try to have grompp observe the particle
>>> density and guide the default of -rdd accordingly?
>>> 
>>> Mark
>>> 
>>> On Wed, Mar 23, 2016 at 9:19 AM Tsjerk Wassenaar 
>>> wrote:
>>> 
 Hi James,
 
 Try setting -rdd 1.4 in mdrun. Sometimes 1.5 or 1.6 is necessary
 (especially if you use a larger time step, like 30 fs).
 
 Cheers,
 
 Tsjerk
> On Mar 23, 2016 09:08, "James Starlight"  wrote:
> 
> Hello,
> 
> 
> I am trying to perform 2 MARTINI simulations of several membrane
> receptors within membrane i) with eldyn restrains applied on the
> protein tetriary structure and ii) unrestrained md. I have no problems
> in the i) case but in the ii) my simulation is very unstable under
> pruduction run- it begins OK after long period of equilibration but
> suddenly is crashed after 20-50ns of C run although I reduced the
> integration time-step twisely in comparison to restrained run  (0.005
> vs 0.01)
> 
> Fatal error:
> 1 of the 20932 bonded interactions could not be calculated because
> some atoms involved moved further apart than the multi-body cut-off
> distance (1.2 nm) or the two-body cut-off distance (1.2 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
> 
> might another tricks be used here besides elastic restraints consisted
> of mostly of md simulation setups e.g switching to the another
> termostat (right now martini uses berendsen with gmx 4.5) e.g ussing
> of sd integraator instead7
> 
> Thanks for help!
> 
> James
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Re: [gmx-users] Gromacs Tutorial

[XAvier Periole]

Bastards … 

On Jan 19, 2016, at 2:00 PM, Tsjerk Wassenaar  wrote:

> Hey :)
> 
> As some of you know, some years ago I developed an extensive Gromacs
> tutorial (at the University of Utrecht). That work has caught they eye of
> educators, and now the tutorial is published as an educational paper! Just
> kind of funny that I'm not an author.
> For those interested:
> 
> http://onlinelibrary.wiley.com/doi/10.1002/bmb.20941/abstract
> 
> Enjoy!
> 
> Tsjerk
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] regarding glycolipids parameters for GROMACS

[Xavier Periole]

Hi, 

A set of exotic lipids compatible with GROMOS should be available soon too :)).

XAvier. 



> On Mar 3, 2015, at 23:06, Carlos Navarro Retamal  wrote:
> 
> Dear gromacs users,
> I was wondering, are they glycolipids (MGDG more specifically) parameters 
> availably for gromacs package? it doesn’t matter for which forcefield they 
> were constructed.
> Kind regards,
> Carlos
> 
> --
> Carlos Navarro Retamal
> Bioinformatics Engineering
> Ph. D (c) Applied Sciences.
> Center of Bioinformatics and Molecular Simulations. CBSM
> University of Talca
> Av. Lircay S/N, Talca, Chile
> T: (+56) 712201 798
> E: carlos.navarr...@gmail.com or cnava...@utalca.cl
> 
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Re: [gmx-users] clustering using gromos method

[XAvier Periole]

Yes, should work.

Check that the central structures make sense. At some point this option was not 
giving the correct structure. 

On Jan 13, 2015, at 1:32 PM, Adriana Garro  wrote:

> Another question just to be sure that I get what I want.
> I want the structure with the smallest average distance to the others (The
> center of a cluster) for each cluster written in the clusters.pdb file
> (option -cl), but after calculation I get this message in the log file
> 
> 
> "Writing middle structure for each cluster to clusters.pdb"
> 
> is it ok??
> 
> the command line I used
> g_cluster -f dynamic.xtc -s dynamic.tpr -o cluster.xpm -minstruct 20 -sz
> cluster-sizes.xvg -clid cluster-id-over-time.xvg -cl clusters.pdb -cutoff
> 0.3 -method gromos -skip 10 -dist rms-distribution.xvg -noav
> 
> Thanks for your time!
> 
> Adriana
> 
> 
> ***
> Dra. Adriana D. Garro
> Química Medicinal
> Facultad de Química, Bioquímica y Farmacia
> Universidad Nacional de San Luis
> IMASL-CONICET
> San Luis, Argentina
> 
> Tel..:+54 266 4424689  int 6153
> e-mail...: adga...@unsl.edu.ar
> e-mail...:  adrianagarr...@gmail.com
> 
> 
> **
> 
> 2015-01-13 9:46 GMT+01:00 Adriana Garro :
> 
>> Thanks for the reply Xavier.
>> Cheers,
>> 
>> Adriana
>> 
>> ***
>> Dra. Adriana D. Garro
>> Química Medicinal
>> Facultad de Química, Bioquímica y Farmacia
>> Universidad Nacional de San Luis
>> IMASL-CONICET
>> San Luis, Argentina
>> 
>> Tel..:+54 266 4424689  int 6153
>> e-mail...: adga...@unsl.edu.ar
>> e-mail...:  adrianagarr...@gmail.com
>> 
>> 
>> **
>> 
>> 2015-01-12 17:12 GMT+01:00 XAvier Periole :
>> 
>>> 
>>> with the gromos method the criteria is the RMSD between the structure of
>>> the objects given to cluster …. two neighbours are two structures that are
>>> within this cutoff (eg. 0.25)
>>> 
>>> obviously defining an RMSD between the two objects should make sense.
>>> 
>>> On Jan 12, 2015, at 4:56 PM, Adriana Garro 
>>> wrote:
>>> 
>>>> Dear All,
>>>> 
>>>> I am working on a Coarse Grained model (Martini force field), I have a
>>>> trajectory file and
>>>> I am trying to do a clustering procedure using the gromos method, this
>>> is
>>>> the command line I used
>>>> 
>>>> g_cluster -f dynamic.xtc -s dynamic.tpr -o cluster.xpm -clid
>>>> cluster-id-over-time.xvg -cl clusters.pdb -cutoff 0.25 -method gromos
>>> -skip
>>>> 10
>>>> 
>>>> and it finished well, I got more than 40 clusters, of course if I vary
>>> the
>>>> cutoff this number changes but I am not sure what is the more optimal
>>> value
>>>> for my system. In fact I dont understand very well what is the meaning
>>> of
>>>> this parameter.
>>>> I have read this
>>>> "gromos: use algorithm as described in Daura et al. (Angew. Chem. Int.
>>> Ed.
>>>> *1999*, 38, pp 236-240). Count number of neighbors using cut-off, take
>>>> structure with largest number of *neighbors* with all its neighbors as
>>>> cluster and eliminate it from the pool of clusters. Repeat for remaining
>>>> structures in pool."
>>>> But still...what neighbors means in this context?
>>>> If someone can clarify this for me, I'd really appreciate it. (I cant
>>> acces
>>>> to the original publication).
>>>> Thanks in advance.
>>>> 
>>>> Adriana
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>>&

Re: [gmx-users] clustering using gromos method

[XAvier Periole]

with the gromos method the criteria is the RMSD between the structure of the 
objects given to cluster …. two neighbours are two structures that are within 
this cutoff (eg. 0.25) 

obviously defining an RMSD between the two objects should make sense.

On Jan 12, 2015, at 4:56 PM, Adriana Garro  wrote:

> Dear All,
> 
> I am working on a Coarse Grained model (Martini force field), I have a
> trajectory file and
> I am trying to do a clustering procedure using the gromos method, this is
> the command line I used
> 
> g_cluster -f dynamic.xtc -s dynamic.tpr -o cluster.xpm -clid
> cluster-id-over-time.xvg -cl clusters.pdb -cutoff 0.25 -method gromos -skip
> 10
> 
> and it finished well, I got more than 40 clusters, of course if I vary the
> cutoff this number changes but I am not sure what is the more optimal value
> for my system. In fact I dont understand very well what is the meaning of
> this parameter.
> I have read this
> "gromos: use algorithm as described in Daura et al. (Angew. Chem. Int. Ed.
> *1999*, 38, pp 236-240). Count number of neighbors using cut-off, take
> structure with largest number of *neighbors* with all its neighbors as
> cluster and eliminate it from the pool of clusters. Repeat for remaining
> structures in pool."
> But still...what neighbors means in this context?
> If someone can clarify this for me, I'd really appreciate it. (I cant acces
> to the original publication).
> Thanks in advance.
> 
> Adriana
> -- 
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Re: [gmx-users] During minimization "A charge group moved too far between two domain decomposition steps"

[XAvier Periole]

The warning of grompp says you have two charge groups (bound groups from a 
molecule) at 7 nm, while the cutoff of theses interactions is 1 nm! This most 
likely reflects a broken molecule … 

Visualising your system indicates it is broken all over the place at the PBC. 
Make your molecule whole first, then solvate it and minimise it. 

The construction of your system is the problem.

On Jan 11, 2015, at 1:36 AM, Jonathan Saboury  wrote:

> Not likely Xavier. It isn't a single water acting unusual. It is many
> waters (probably all) and all biotins making odd angles/lengths.
> 
> Nevertheless I tried the suggestion and I am getting different results, but
> not sure if they are good results.
> 
> "vmd rebuilt_system.gro em.xtc" shows the system but now there are
> undertemined white dot coordinates surrounding the system. Another curious
> thing is that no atoms are moving in those 16 frames.
> 
> As you can see in the mdrun output the minimization finishes but:
> --
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 10
> --
> 
> I read "
> http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision";
> and Epot is not at right range.
> 
> Commands used: http://pastebin.com/raw.php?i=YjTDnzUQ
> grompp output: http://pastebin.com/raw.php?i=TLtT8tcF
> mdrun output: http://pastebin.com/raw.php?i=YTa09GVE
> 
> rebuilt_system.gro (481 KB): http://ge.tt/9khqEL82/v/0
> em.xtc(1.4 MB): http://ge.tt/5zI9FL82/v/0
> 
> Thank you!
> 
> On Sat, Jan 10, 2015 at 3:17 PM, Jonathan Saboury  wrote:
> 
>> My system is blowing up during minimization. I'm getting the error:
>> -
>> Fatal error:
>> A charge group moved too far between two domain decomposition steps
>> This usually means that your system is not well equilibrated
>> -
>> 
>> I looked at "http://www.gromacs.org/Documentation/Terminology/Blowing_Up";
>> with no solution. I am minimizing the system to prevent blowing up, but it
>> is blowing up in the energy minimization. Bad starting structure is
>> unlikely because water is showing unusual bond angles and lengths far from
>> any biotin or protein atoms (in system.gro+em.xtc files).
>> 
>> I found it unusual that atom names in system.top did not match with
>> system.gro (as seen in the grompp output).
>> 
>> Second warning is:
>> --
>> WARNING 2 [file em.mdp]:
>>  The sum of the two largest charge group radii (15.152546) is larger than
>>  rlist (1.00)
>> --
>> No idea what that means though.
>> 
>> Any ideas? Thank you!
>> 
>> commands used: http://pastebin.com/raw.php?i=ea4dUNT6
>> grompp output: http://pastebin.com/raw.php?i=gtHwdhuM
>> em.mdp (.mdp used for minimization):
>> http://pastebin.com/raw.php?i=sRnEMA5F
>> system.gro + em.xtc(3.8 MB): http://ge.tt/9E7i1L82/v/0
>> All files (15 MB): http://ge.tt/8FCb2L82/v/0
>> 
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Re: [gmx-users] During minimization "A charge group moved too far between two domain decomposition steps"

[XAvier Periole]

Could be a water molecule broken at the box limits. Try to rebuild the water 
molecules before minimizing. Trjconv -pbc mol -f in.gro -o out.gro would do it. 



> On Jan 11, 2015, at 00:17, Jonathan Saboury  wrote:
> 
> My system is blowing up during minimization. I'm getting the error:
> -
> Fatal error:
> A charge group moved too far between two domain decomposition steps
> This usually means that your system is not well equilibrated
> -
> 
> I looked at "http://www.gromacs.org/Documentation/Terminology/Blowing_Up";
> with no solution. I am minimizing the system to prevent blowing up, but it
> is blowing up in the energy minimization. Bad starting structure is
> unlikely because water is showing unusual bond angles and lengths far from
> any biotin or protein atoms (in system.gro+em.xtc files).
> 
> I found it unusual that atom names in system.top did not match with
> system.gro (as seen in the grompp output).
> 
> Second warning is:
> --
> WARNING 2 [file em.mdp]:
>  The sum of the two largest charge group radii (15.152546) is larger than
>  rlist (1.00)
> --
> No idea what that means though.
> 
> Any ideas? Thank you!
> 
> commands used: http://pastebin.com/raw.php?i=ea4dUNT6
> grompp output: http://pastebin.com/raw.php?i=gtHwdhuM
> em.mdp (.mdp used for minimization): http://pastebin.com/raw.php?i=sRnEMA5F
> system.gro + em.xtc(3.8 MB): http://ge.tt/9E7i1L82/v/0
> All files (15 MB): http://ge.tt/8FCb2L82/v/0
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Re: [gmx-users] martinize.py: option for partly have elastic network on partly in the protein

[XAvier Periole]

There is no specific option to do this but you can go in the itp file where the 
electric network is defined and comment out the section corresponding to the 
n-terminus. 

> On Dec 18, 2014, at 14:57, shivangi nangia  wrote:
> 
> Dear gmx-users,
> 
> I wish to coarse grain a  peptide, while keeping only the N-terminal
> flexible (elastic network off) and rest protein elastic on.
> 
> Is there any option/flag to selectively pick residues on which I do not
> want elastic network on.
> 
> Kindly suggest.
> 
> Thanks in advance,
> sxn
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Re: [gmx-users] Martini force field for inhibitors

[XAvier Periole]

There are a few review article where the strategy and guidelines are described. 
You can find this material on the cgmartini.nl website. 

> On Aug 29, 2014, at 2:03, Sridhar Kumar Kannam  wrote:
> 
> Dear Gromacs users,
> 
> I have very recently started working with  Gromacs and Martini force field.
> I am able to generate the coarse-grained model for HIV Protease (1hvr.pdb).
> I want to simulate the protein along with its inhibitor. Are there any
> guidelines for building (coarse-graining) its inhibitor ?
> 
> Sorry for the naive question ...
> 
> Thank you.
> 
> 
> 
> 
> 
> 
> -- 
> Cheers !!!
> Sridhar  Kumar Kannam :)
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Re: [gmx-users] Archaeal lipid packages for Gromos 53A6

[XAvier Periole]

If you want to stick to the GROMOS force field family you'd want to use the 
gromos-54A7/8
J. Chem. Theory Comput., 2013, 9 (2), pp 1247–1264, 
DOI: 10.1021/ct300874c

CHARMM over-stabilizes helices. 

On Aug 12, 2014, at 5:12 PM, Justin Lemkul  wrote:

> 
> 
> On 8/12/14, 11:08 AM, Wainwright, Josh wrote:
>> Thanks for the prompt response Justin. We are working with protein fragments 
>> with between 1 and 3 helices.
>> 
>> I've noticed that Anirban Ghosh made a tutorial based on yours, and he used 
>> Gromos43a1 for a GPCR (7 helices) in bacterial membranes (POPC in his case, 
>> as opposed to DPPC in your case with the model KALP-15 protein). Do you 
>> think 43a1 is a good alternative, or is there any other forcefield you would 
>> recommend?
>> 
> 
> 43A1 or 54A7 would probably be better.
> 
>> I've also seen people recommend CHARMM36.
>> 
> 
> CHARMM36 has excellent lipid parameters, better than Berger for most 
> observables.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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] Use g_wham on 2D PMF

[XAvier Periole]

g_wham does only 1D PMF but can handle several restrains. 

There is 2D code on Alan Grossfield website. Plumed refers to it. 

On Feb 3, 2014, at 5:54 PM, "DAI, JIAN"  wrote:

> Dear all:
> Is it possible for g_wham to calculate 2D PMF? 
> It seems to me that g_wham can deal with this because the example for the pdo 
> files in the g_wham documentation has two groups and it says that it can 
> handle up to four pull groups.
> Say I have a bunch of time series for two variables in different folders, and 
> after running g_wham using the -ip option I got histo.xvg and profile.xvg, 
> but neither of these two seems to contain information of a free energy 
> landscape. Do I miss something?
> Another question: Using wham-2d we are able to get the free energy landscape. 
> We also want to do bootstrap analysis of the variation range of the 2D PMF, 
> but I'm not sure how to do that? Naively I thought of generating bootstrap 
> sample for each window, do WHAM-2d and calculate the variation. Is this 
> correct?
> Thank you.
> Jian
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Re: [gmx-users] Bond interaction exclusions

[XAvier Periole]

Hi, 

The first line "eth1" tells it all. In that molecule all non-bonded 
interactions between first bonded neighbors will be excluded. 

Thus the 1-3, 1-4 (and so on) non-bonded interactions will be included. You may 
add additional exclusions in the [ exclusion ] section of your topology. 

I am not sure what you mean with 1-4 bonded interactions but if you mean 
non-bonded then see above. 

> On Feb 2, 2014, at 17:29, Xu Dong Huang  wrote:
> 
> Dear all,
> 
> I am unclear about the bond exclusion properties within gromacs. Using a 
> martini model system, what is the default behavior of setting 
> [moleculetype]
> ;nameexclusions
> eth  1
> 
> exclusions to 1? How do I find out what kind of interaction it is excluding? 
> I am interested in finding out if this is excluding 1-3 interaction or 1-4 
> interaction. I guess what I also want to know is if my settings are including 
> 1-4 bonded interactions or using only 1-3. 
> 
> Please let me know,
> 
> thank you. 
> 
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Re: [gmx-users] charge correction in topology file from PRODRG

[XAvier Periole]

For gromos ff you can also use the ATB server. From Alan Mark on Brisbane. It 
combine typography and non-bonded parameters all at once. 

It is not perfect but pretty good. 

> On Dec 8, 2013, at 8:27, Mahboobeh Eslami  wrote:
> 
> hi all my friends
> I use PRODRG and antechmber for building topology and coordinate files for my 
> ligand separately.
> i want to use GROMOS force field so i must to use the topology from PRODRG 
> server. can i use the topology of antechamber for charge correction in 
> topology fiel from PRODRG .
> In general, are special principlesessential for charge correction in topology 
> file from PRODRG 
>  thanks for your help
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Re: [gmx-users] end capping

[XAvier Periole]

You can choose different termini by setting the option term (-term) to pdb2gmx. 

The ff gromos 53a6 has a strong tendency to destabilize alpha helices and 
favors sheets. If you like to stick to gromos ff you need to switch to the 54a7 
more recent version to which a rectification of this bias has been attempt. 

> On Dec 7, 2013, at 14:11, Shine A  wrote:
> 
> Sir,
> 
>I am using MD to study the folding of peptides. Now I want to
> modify N terminal of the peptide with acetyl group and C terminus with
> amide group.How Can I do this? What are the changes I should made in
> various files? Gromos96 53a6 is using for simulation.
> 
> 
> 
> Thank in advance
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Re: [gmx-users] # of threads different than # of cores -> gmx hangs.

[XAvier Periole]

OK, I'll try to get that tomorrow if not next week. 

In my case the issue was not to be able to run a mixture of 23 and 24 threads 
on a set of nodes with 24 CPUs. A few nodes had 23 threads assigned, the rest 
24, per node. moving to 23 or 24 threads per node for all nodes fixed the issue.

XAvier.

On Nov 26, 2013, at 6:43 PM, Mark Abraham  wrote:

> OK, thanks. We would like to fix that so that it does not hang, but we
> might need to know some more details. So far, I have failed to replicate
> your symptoms using 30 threads across 2 nodes with 32 total cores. However,
> my mpirun and/or OpenMP library was setting thread affinities for me. That
> may or may not have been the case for you. Can you please open an issue at
> redmine.gromacs.org with .tpr, .log, stdout, stderr for both a working and
> failing case?
> 
> Mark
> 
> 
> On Mon, Nov 25, 2013 at 3:25 PM, XAvier Periole  wrote:
> 
>> 
>> For the record.
>> 
>> gmx-4.6.4 hangs when number of threads is not a multiple of the number of
>> nodes.
>> 
>> XAvier.
>> 
>> On Nov 22, 2013, at 7:14 PM, XAvier Periole  wrote:
>> 
>>> 
>>> Ok, tks. I'll try then :))
>>> 
>>> XAvier.
>>> 
>>> On Nov 22, 2013, at 4:31 PM, Mark Abraham 
>> wrote:
>>> 
>>>> Hardware detection and management of the results is greatly improved
>> since
>>>> 4.6.1, so we would expect relevant changes, particularly if -pin off
>> makes
>>>> it work (very slowly)
>>>> 
>>>> Mark
>>>> On Nov 21, 2013 7:37 PM, "XAvier Periole"  wrote:
>>>> 
>>>>> 
>>>>> For the record:
>>>>> 
>>>>> I do not expect this issue to be affected by an update to gmx4.6.4 …
>>>>> 
>>>>> But the problem is fixed by turning the pin option off.
>>>>> 
>>>>> XAvier.
>>>>> 
>>>>> On Nov 21, 2013, at 6:04 PM, Szilárd Páll 
>> wrote:
>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> It's not expected, but instead of trying to figure out what the issues
>>>>>> is with 4.6.1, you should really update to the latest version. If the
>>>>>> problem persists with 4.6.4, we shall have a closer look.
>>>>>> 
>>>>>> Cheers,
>>>>>> --
>>>>>> Szilárd
>>>>>> 
>>>>>> 
>>>>>> On Thu, Nov 21, 2013 at 11:38 AM, XAvier Periole 
>>>>> wrote:
>>>>>>> 
>>>>>>> Dears,
>>>>>>> 
>>>>>>> When running on multiple nodes I get GMX-461 hanging if the number of
>>>>> threads is not a multiple of the number of cores.
>>>>>>> 
>>>>>>> example: with 11 nodes having 24 cores each, defining 253 threads (23
>>>>> threads per node) or 264 threads (24 threads per node) would work but
>>>>> defining 256 threads would result in mdrun to hang for long time.
>>>>>>> 
>>>>>>> That might be expected and not really an issue but that be nice if
>>>>> anyone knows why.
>>>>>>> 
>>>>>>> Thanks,
>>>>>>> XAvier.
>>>>>>> --
>>>>>>> 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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>>>>>>> 
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>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
>>>>> send a mail to gmx-users-requ...@gromacs.org.
>>>>>> --
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>>>>>> 
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>>>>> send a mail to gmx-users-requ...@gromacs.o

Re: [gmx-users] # of threads different than # of cores -> gmx hangs.

[XAvier Periole]

For the record.

gmx-4.6.4 hangs when number of threads is not a multiple of the number of 
nodes. 

XAvier.

On Nov 22, 2013, at 7:14 PM, XAvier Periole  wrote:

> 
> Ok, tks. I'll try then :))
> 
> XAvier.
> 
> On Nov 22, 2013, at 4:31 PM, Mark Abraham  wrote:
> 
>> Hardware detection and management of the results is greatly improved since
>> 4.6.1, so we would expect relevant changes, particularly if -pin off makes
>> it work (very slowly)
>> 
>> Mark
>> On Nov 21, 2013 7:37 PM, "XAvier Periole"  wrote:
>> 
>>> 
>>> For the record:
>>> 
>>> I do not expect this issue to be affected by an update to gmx4.6.4 …
>>> 
>>> But the problem is fixed by turning the pin option off.
>>> 
>>> XAvier.
>>> 
>>> On Nov 21, 2013, at 6:04 PM, Szilárd Páll  wrote:
>>> 
>>>> Hi,
>>>> 
>>>> It's not expected, but instead of trying to figure out what the issues
>>>> is with 4.6.1, you should really update to the latest version. If the
>>>> problem persists with 4.6.4, we shall have a closer look.
>>>> 
>>>> Cheers,
>>>> --
>>>> Szilárd
>>>> 
>>>> 
>>>> On Thu, Nov 21, 2013 at 11:38 AM, XAvier Periole 
>>> wrote:
>>>>> 
>>>>> Dears,
>>>>> 
>>>>> When running on multiple nodes I get GMX-461 hanging if the number of
>>> threads is not a multiple of the number of cores.
>>>>> 
>>>>> example: with 11 nodes having 24 cores each, defining 253 threads (23
>>> threads per node) or 264 threads (24 threads per node) would work but
>>> defining 256 threads would result in mdrun to hang for long time.
>>>>> 
>>>>> That might be expected and not really an issue but that be nice if
>>> anyone knows why.
>>>>> 
>>>>> Thanks,
>>>>> XAvier.
>>>>> --
>>>>> 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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>>>>> 
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>>>>> 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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>>> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Martini and Gromacs 3 and 4

[XAvier Periole]

Yes you can use MARTINI with any GMX. 

On Nov 22, 2013, at 8:16 PM, Steve Seibold  wrote:

> Hello
> I was under the impression that I needed Gromacs 3.3.1 to implement the 
> Martini FF. But as I have been looking at mdp files for Martini, I am finding 
> statements about this mdp file to be used for Gromacs 4. I must be 
> missunderstanding something here...Can I use Gromacs 4.5.4 to run Martini FF?
> 
> Thanks, Steve
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Re: [gmx-users] # of threads different than # of cores -> gmx hangs.

[XAvier Periole]

Ok, tks. I'll try then :))

XAvier.

On Nov 22, 2013, at 4:31 PM, Mark Abraham  wrote:

> Hardware detection and management of the results is greatly improved since
> 4.6.1, so we would expect relevant changes, particularly if -pin off makes
> it work (very slowly)
> 
> Mark
> On Nov 21, 2013 7:37 PM, "XAvier Periole"  wrote:
> 
>> 
>> For the record:
>> 
>> I do not expect this issue to be affected by an update to gmx4.6.4 …
>> 
>> But the problem is fixed by turning the pin option off.
>> 
>> XAvier.
>> 
>> On Nov 21, 2013, at 6:04 PM, Szilárd Páll  wrote:
>> 
>>> Hi,
>>> 
>>> It's not expected, but instead of trying to figure out what the issues
>>> is with 4.6.1, you should really update to the latest version. If the
>>> problem persists with 4.6.4, we shall have a closer look.
>>> 
>>> Cheers,
>>> --
>>> Szilárd
>>> 
>>> 
>>> On Thu, Nov 21, 2013 at 11:38 AM, XAvier Periole 
>> wrote:
>>>> 
>>>> Dears,
>>>> 
>>>> When running on multiple nodes I get GMX-461 hanging if the number of
>> threads is not a multiple of the number of cores.
>>>> 
>>>> example: with 11 nodes having 24 cores each, defining 253 threads (23
>> threads per node) or 264 threads (24 threads per node) would work but
>> defining 256 threads would result in mdrun to hang for long time.
>>>> 
>>>> That might be expected and not really an issue but that be nice if
>> anyone knows why.
>>>> 
>>>> Thanks,
>>>> XAvier.
>>>> --
>>>> 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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>>>> 
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>>>> 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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Re: [gmx-users] # of threads different than # of cores -> gmx hangs.

[XAvier Periole]

For the record:

I do not expect this issue to be affected by an update to gmx4.6.4 … 

But the problem is fixed by turning the pin option off.

XAvier.

On Nov 21, 2013, at 6:04 PM, Szilárd Páll  wrote:

> Hi,
> 
> It's not expected, but instead of trying to figure out what the issues
> is with 4.6.1, you should really update to the latest version. If the
> problem persists with 4.6.4, we shall have a closer look.
> 
> Cheers,
> --
> Szilárd
> 
> 
> On Thu, Nov 21, 2013 at 11:38 AM, XAvier Periole  wrote:
>> 
>> Dears,
>> 
>> When running on multiple nodes I get GMX-461 hanging if the number of 
>> threads is not a multiple of the number of cores.
>> 
>> example: with 11 nodes having 24 cores each, defining 253 threads (23 
>> threads per node) or 264 threads (24 threads per node) would work but 
>> defining 256 threads would result in mdrun to hang for long time.
>> 
>> That might be expected and not really an issue but that be nice if anyone 
>> knows why.
>> 
>> Thanks,
>> XAvier.
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[gmx-users] # of threads different than # of cores -> gmx hangs.

[XAvier Periole]

Dears,

When running on multiple nodes I get GMX-461 hanging if the number of threads 
is not a multiple of the number of cores.

example: with 11 nodes having 24 cores each, defining 253 threads (23 threads 
per node) or 264 threads (24 threads per node) would work but defining 256 
threads would result in mdrun to hang for long time.

That might be expected and not really an issue but that be nice if anyone knows 
why. 

Thanks,
XAvier.
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Re: [gmx-users] MD simulations in the presence of osmolytes

[XAvier Periole]

That would be a question for the developers of the force fields. You can start 
by a google search of the osmolytes and force filed keywords ... 

> On Nov 19, 2013, at 2:23, Amjad Farooq  wrote:
> 
> Hi everyone,
> 
> I am wondering whether it is possible to conduct MD simulations on a
> protein system in the presence of osmolytes such as TMAO and sucrose using
> an explicit water model.
> 
> If not, how could this be implemented?
> 
> Does any of the force fields available in GROMACS support the inclusion of
> any of these osmolytes?
> 
> Thank you for your input.
> 
> 
> 
> 
> *AMJAD FAROOQ PhD DIC | Associate ProfessorDept of Biochemistry & Molecular
> Biology | Miller School of Medicine | University of Miami | Miami | FL
> 33136Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217,
> Miami , FL 33136 am...@farooqlab.net  | off
> 305-243-2429 | lab 305-243-9799 | fax 305-243-3955 | www.farooqlab.net
> *
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