Re: [gmx-users] Simulation crashed, fatal error: Bond length not finite and warning: Pressure scaling more than 1%.

[Kroon, P.C.]

You equilibrations are probably too short. There are some pretty slow
processes in lipid membranes.

Peter

On Fri, May 25, 2018 at 6:00 PM, Quyen V. Vu  wrote:

> Hi Zeined,
> Have you check the energy , the box fluctuations and pressure deviations ?
> Best,
> Quyen
>
>
>
> On Fri, May 25, 2018 at 6:30 PM, zeineb SI CHAIB 
> wrote:
>
> > Dear GMX users,
> >
> >
> > I'm running a coarse-grained simulation of a homo-dimer in a membrane
> > composed of POPC, POPE, and CHOL (31%, 41%, 28% respectively), using
> > MARTINI force field and GROMACS software.
> >
> >
> > I followed the usual steps with 1ns minimization, 50 ns NVT equilibration
> > followed by 50ns NPT equilibration.
> >
> >
> > After running 2.5μs of simulation on a cluster, the system crashed with a
> > fatal error:
> >
> >
> > Step 108657121  Warning: Pressure scaling more than 1%. This may mean
> your
> > system is
> >
> > not yet equilibrated. Use of Parrinello-Rahman pressure coupling during
> >
> > equilibration can lead to simulation instability and is discouraged.
> >
> >
> > Fatal error:
> >
> > Bond length not finite.
> >
> >
> > When I analyzed the pressure and the temperature they seem OK. Pressure
> > average = 1.04 bar and Temperature average 314.835 K
> >
> >
> > I don't know what I'm missing and can't diagnose the problem.
> >
> >
> > Any help, please?
> >
> >
> > Thank you in advance for your help and consideration.
> >
> >
> >
> >
> > NB: I used the following MDP parameters for the production run (They are
> > the optimal parameters to run with MARTINI FF):
> >
> >
> > ; TIMESTEP IN MARTINI
> >
> > ; Most simulations are numerically stable with dt=40 fs,
> >
> > ; however better energy conservation is achieved using a
> >
> > ; 20-30 fs time step.
> >
> > ; Time steps smaller than 20 fs are not required unless specifically
> > stated in the itp file.
> >
> >
> > integrator  = md
> >
> > dt= 0.02
> >
> > nsteps= 5000
> >
> >
> > nstxout  = 100
> >
> > nstvout  = 100
> >
> > nstfout  = 0
> >
> > nstlog= 1000
> >
> > nstenergy= 100
> >
> > nstxout-compressed   = 1000
> >
> > compressed-x-precision   = 100
> >
> >
> > continuation   = yes ; Restarting after NPT
> >
> >
> > ; NEIGHBOR LIST and MARTINI
> >
> > ; To achieve faster simulations in combination with the Verlet-neighbor
> > list
> >
> > ; scheme, Martini can be simulated with a straight cutoff. In order to
> >
> > ; do so, the cutoff distance is reduced 1.1 nm.
> >
> > ; The Verlet neighbor list scheme will automatically choose a proper
> > neighbor list
> >
> > ; length, based on a energy drift tolerance.
> >
> > ;
> >
> > ; Coulomb interactions can alternatively be treated using a
> reaction-field,
> >
> > ; giving slightly better properties.
> >
> > ; Please realize that electrostatic interactions in the Martini model are
> >
> > ; not considered to be very accurate, to begin with, especially as the
> >
> > ; screening in the system is set to be uniform across the system with
> >
> > ; a screening constant of 15. When using PME, please make sure your
> >
> > ; system properties are still reasonable.
> >
> >
> > cutoff-scheme= Verlet
> >
> > nstlist  = 20
> >
> > ns_type  = grid
> >
> > pbc  = xyz
> >
> > verlet-buffer-tolerance  = 0.005
> >
> >
> > coulombtype  = reaction-field
> >
> > rcoulomb = 1.1
> >
> > epsilon_r= 15 ; 2.5 (with polarizable water)
> >
> > epsilon_rf   = 0
> >
> > vdw_type = cutoff
> >
> > vdw-modifier = Potential-shift-verlet
> >
> > rvdw = 1.1
> >
> >
> > ; MARTINI and TEMPERATURE/PRESSURE
> >
> > ; Good temperature control can be achieved with the V-rescale
> >
> > ; thermostat using a coupling constant of the order of 1 ps. Even better
> > ; temperature control can be achieved by reducing the temperature
> coupling
> >
> > ; constant to 0.1 ps, although with such tight coupling (approaching
> >
> > ; the time step) one can no longer speak of a weak-coupling scheme.
> >
> > ; We therefore recommend a coupling time constant of at least 0.5 ps.
> >
> > ; The Berendsen thermostat is less suited since it does not give
> >
> > ; a well described thermodynamic ensemble.
> >
> > ;
> >
> > ; Pressure can be controlled with the Parrinello-Rahman barostat,
> >
> > ; with a coupling constant in the range 4-8 ps and typical
> compressibility
> >
> > ; in the order of 10e-4 - 10e-5 bar-1. Note that, for equilibration
> > purposes,
> >
> > ; the Berendsen barostat probably gives better results, as the
> Parrinello-
> >
> > ; Rahman is prone to oscillating behaviour. For bilayer systems the
> > pressure
> >
> > ; coupling should be done semiisotropic.
> >
> >
> > tcoupl  = 

Re: [gmx-users] ion channel in lipid bilayer

[Kroon, P.C.]

True, insane is originally made for Martini, but I *think* it should work
for atomistic as well. Otherwise, make the Martini system with insane,
simulate for a short while, and then convert it to atomistic with
backward.py.

I don't have any experience with charmm-gui myself, so I can't help you
further there.

Peter

On 19 Feb 2018 02:15, "alex rayevsky" <rayevsk...@gmail.com> wrote:

> Dear Peter, thank You for responce!
>
> I've already prepared toplogy file, here is a content:
> 
> ; Include forcefield parameters
> #include "charmm36-jul2017.ff/forcefield.itp"
> #include "/home/dikov/alex/WORK/lipid/charmm36.itp"
> #include "LIG.itp"
>
> ; Include chain topologies
>
> #include "topol_Protein_chain_A.itp"
> #include "topol_Protein_chain_A2.itp"
> #include "topol_Other_chain_A3.itp"
> #include "topol_Protein_chain_B.itp"
> #include "topol_Protein_chain_B2.itp"
> #include "topol_Protein_chain_C.itp"
> #include "topol_Protein_chain_C2.itp"
> #include "topol_Protein_chain_D.itp"
> #include "topol_Protein_chain_D2.itp"
>
> ; Strong position restraints for InflateGRO
> #ifdef STRONG_POSRES
> #include "strong_posre.itp"
> #endif
>
> ; Include POPG chain topology
> #include "POPG.itp"
>
> ; Include water topology
> #include "/home/dikov/alex/WORK/lipid/TIP3.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
>
> ;  i funct   fcxfcyfcz
>11   1000   1000   1000
>
> #endif
>
> ; Include topology for ions
> #include "charmm36-jul2017.ff/ions.itp"
> #include "POT.itp"
>
> [ system ]
> ; Name
> Protein
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_A 1
> Protein_chain_A21
> Other_chain_A3  1
> Protein_chain_B 1
> Protein_chain_B21
> Protein_chain_C 1
> Protein_chain_C21
> Protein_chain_D 1
> Protein_chain_D21
> LIG 1
> POT 118
> POPG96
> '''
>
> Insane script is for Martini, am I right? Charmm-gui was very confusing and
> hard to generate orientation.
> However, if no ohter suggestions available, I'll try Your's!
> Thank You!!
> >>>>
> ___
>
> Kroon, P.C. Sun, 18 Feb 2018 15:52:30 -0800
> <https://www.mail-archive.com/search?l=gromacs.org_gmx-
> us...@maillist.sys.kth.se=date:20180218>
>
> Hi Alex,
>
> Try either insane.py, or charmm-gui. I can't provide links, since I'm on my
> phone.
>
> You may need to generate the topology (itp) of the protein, which you can
> do with calling pdb2gmx on just the protein. You should have a topology
> (itp) of your favourite lipid.
>
> Peter
>
>
>
>
>
>
>
>
> 2018-02-17 0:56 GMT+02:00 alex rayevsky <rayevsk...@gmail.com>:
>
> > Hi all!
> >
> > I have a question concerning immersion of the ion channel (four subunits
> > with extracellular domains and a bundles of helixes)  into the lipid
> > bilayer. 6 years ago I used some tutorial or mailing lists, which
> described
> > the way from KALP15 tutor. With CCR5 model there were no problems at all.
> > Now I have a not 'cylindric'  protein with a complex shape and
> overhanging
> > domains.
> > the forcefield is CHARMM36, lipid type - POPG.
> >
> > I tried Membrane builder, but couldn't orient the plane of the membrane
> by
> > changing XYZ principles many times in different combinations.. Thus I
> used
> > a slightly modified KALP15 method (other .itps, lipids and water
> > molecules).  First of all after pdb2gmx for protein a series of
> > topologies were generated with identifiers in the name, as it was
> assigned
> > in each chain. However editconf produced a new pdb from the outpu gro
> > without any ID or terminators for the chains, in Pymol it is represented
> > with a tetramer entirely highlithing if a single chain is selected (maybe
> > it is a reason of faults at later stages).
> >
> > Well, it works fine until the perl script execution. Beside some problems
> > with the output (system_inflated.gro was corrupted, but I repaired it
> with
> > simple python scripting and got a pretty protein in the center of rare
> > molecules, which looks reliable enough) I started to compact the bilayer
> to
> > rich the lipid area of ~53A^2. I finished it on the 13 stage of perl
> > execution - the distance between nearest lipids was about 16A, however,
> the
> > layer was real

Re: [gmx-users] Fwd: ion channel in lipid bilayer

[Kroon, P.C.]

Hi Alex,

Try either insane.py, or charmm-gui. I can't provide links, since I'm on my
phone.

You may need to generate the topology (itp) of the protein, which you can
do with calling pdb2gmx on just the protein. You should have a topology
(itp) of your favourite lipid.

Peter

On 18 Feb 2018 13:54, "alex rayevsky"  wrote:

> I'm sorry for repeat, but nobody answered the question and I decided to
> duplicate the request. Maybe it is a problem with a form of question or its
> content, please, point me the mistake.
>
> Hi all!
>
> I have a question concerning immersion of the ion channel (four subunits
> with extracellular domains and a bundles of helixes)  into the lipid
> bilayer. 6 years ago I used some tutorial or mailing lists, which described
> the way from KALP15 tutor. With CCR5 model there were no problems at all.
> Now I have a not 'cylindric'  protein with a complex shape and overhanging
> domains.
> the forcefield is CHARMM36, lipid type - POPG.
>
> I tried Membrane builder, but couldn't orient the plane of the membrane by
> changing XYZ principles many times in different combinations.. Thus I used
> a slightly modified KALP15 method (other .itps, lipids and water
> molecules).  First of all after pdb2gmx for protein a series of topologies
> were generated with identifiers in the name, as it was assigned in each
> chain. However editconf produced a new pdb from the outpu gro without any
> ID or terminators for the chains, in Pymol it is represented with a
> tetramer entirely highlithing if a single chain is selected (maybe it is a
> reason of faults at later stages).
>
> Well, it works fine until the perl script execution. Beside some problems
> with the output (system_inflated.gro was corrupted, but I repaired it with
> simple python scripting and got a pretty protein in the center of rare
> molecules, which looks reliable enough) I started to compact the bilayer to
> rich the lipid area of ~53A^2. I finished it on the 13 stage of perl
> execution - the distance between nearest lipids was about 16A, however, the
> layer was really holey. At the same time the protein was not surrounded
> from all sides. But if I try to put lipids closely one to other, they are
> simultaneously penetrate the protein body.
>
> Is it the correct method for such kind of simmulations? Could I increase
> the number of POPG molecules after getting inflated.gro file with scaled up
> bilayer (the initial step for tightning) before scaling iterations? I can
> do it manually by copy of the layer (all lipid coordinates) and its
> rotation around Y axis in any soft to enlarge the number of molecules in
> the cell (even 200 mols is more than 128). Of course I will make changes in
> a topology file. It seems, that I will obtain a fully wrapped protein
> without anxiety about clashes or presure in cavities...
>
> What do You think? Thank You in advance!
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates

[Kroon, P.C.]

Hi,

I don't have an example at hand, but I'll remember!
Thanks for the hard work :)

Peter

On Mon, Feb 6, 2017 at 10:08 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> If so, please share a case on https://redmine.gromacs.org that doesn't
> work
> as you think it should. We're very happy to make things work better!
>
> Mark
>
> On Mon, 6 Feb 2017 10:04 Kroon, P.C. <p.c.kr...@rug.nl> wrote:
>
> > Alternatively, center it on an interfacial residue. pbc cluster doesn't
> > always work, unfortunately.
> >
> > Peter
> >
> > On Sat, Feb 4, 2017 at 7:56 PM, Christopher Neale <
> > chris.ne...@alum.utoronto.ca> wrote:
> >
> > > Awesome Mark, thanks! It works.
> > >
> > > I filed a bug about a nonexistent -clustercenter option mentioned in
> the
> > > v5.1.2 help file, but the command seems to work anyway for my usage.
> > >
> > > Thanks again,
> > > Chris.
> > > 
> > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> > > Abraham <mark.j.abra...@gmail.com>
> > > Sent: 04 February 2017 07:27:52
> > > To: Discussion list for GROMACS users
> > > Subject: Re: [gmx-users] how to reimage PBC based on distance to a
> given
> > > selection without recentering or otherwise changing atomic coordinates
> > >
> > > Hi,
> > >
> > > I've never really use it myself, but I imagine trjconv -pbc cluster is
> > > useful for this kind of scenario when you want to treat a group of
> > > molecules as indivisible.
> > >
> > > Mark
> > >
> > > On Sat, 4 Feb 2017 09:33 Christopher Neale <
> chris.ne...@alum.utoronto.ca
> > >
> > > wrote:
> > >
> > > > Dear users:
> > > >
> > > > I have a system in which molecule A is in direct contact with
> molecule
> > B.
> > > > However, molecule B is imaged in a different periodic cell. What I
> > would
> > > > like to do is to get an image of both molecules in a periodic
> > > > representation in which they actually are in contact (i.e., reimage
> > > > molecule B such that it is closest to molecule A). However, I do not
> > want
> > > > to lose spatial information with e.g. a trjconv -center -pbc mol
> > command.
> > > >
> > > > This is part of a complex automated build procedure and I can get
> into
> > > > more details if that is useful, but the crux is that I am extracting
> a
> > > > frame from a simulation, building more atoms onto molecule A, and
> > setting
> > > > up a new simulation. To build onto molecule A, I want to then do a
> > vacuum
> > > > EM before adding it back to the water box, for which I first enlarge
> > the
> > > > vacuum box, and changing box dimensions is messing with the
> periodicity
> > > and
> > > > throwing molecule B away from molecule A in an unrealistic fashion
> > > > (molecule B is a tightly bound ligand).
> > > >
> > > > I could do what I want by breaking each molecule out into its own
> box,
> > > > checking for contacts, reimaging, and then putting them back
> together.
> > I
> > > > presume (but have not checked) that I could also do this by making a
> > new
> > > > .itp file in which both molecule A and B are part of the same [
> > molecule
> > > ]
> > > > definition and then running a zero-step mdrun. However, I am writing
> to
> > > see
> > > > if anybody knows how reimage based on a selection (would be a single
> > atom
> > > > in molecule A near the contact between molecule A and B) more
> elegantly
> > > > with processing tools available in gromacs.
> > > >
> > > > Thank you for your help,
> > > > Chris.
> > > > --
> > > > 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.or

Re: [gmx-users] how to reimage PBC based on distance to a given selection without recentering or otherwise changing atomic coordinates

[Kroon, P.C.]

Alternatively, center it on an interfacial residue. pbc cluster doesn't
always work, unfortunately.

Peter

On Sat, Feb 4, 2017 at 7:56 PM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> Awesome Mark, thanks! It works.
>
> I filed a bug about a nonexistent -clustercenter option mentioned in the
> v5.1.2 help file, but the command seems to work anyway for my usage.
>
> Thanks again,
> Chris.
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: 04 February 2017 07:27:52
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] how to reimage PBC based on distance to a given
> selection without recentering or otherwise changing atomic coordinates
>
> Hi,
>
> I've never really use it myself, but I imagine trjconv -pbc cluster is
> useful for this kind of scenario when you want to treat a group of
> molecules as indivisible.
>
> Mark
>
> On Sat, 4 Feb 2017 09:33 Christopher Neale 
> wrote:
>
> > Dear users:
> >
> > I have a system in which molecule A is in direct contact with molecule B.
> > However, molecule B is imaged in a different periodic cell. What I would
> > like to do is to get an image of both molecules in a periodic
> > representation in which they actually are in contact (i.e., reimage
> > molecule B such that it is closest to molecule A). However, I do not want
> > to lose spatial information with e.g. a trjconv -center -pbc mol command.
> >
> > This is part of a complex automated build procedure and I can get into
> > more details if that is useful, but the crux is that I am extracting a
> > frame from a simulation, building more atoms onto molecule A, and setting
> > up a new simulation. To build onto molecule A, I want to then do a vacuum
> > EM before adding it back to the water box, for which I first enlarge the
> > vacuum box, and changing box dimensions is messing with the periodicity
> and
> > throwing molecule B away from molecule A in an unrealistic fashion
> > (molecule B is a tightly bound ligand).
> >
> > I could do what I want by breaking each molecule out into its own box,
> > checking for contacts, reimaging, and then putting them back together. I
> > presume (but have not checked) that I could also do this by making a new
> > .itp file in which both molecule A and B are part of the same [ molecule
> ]
> > definition and then running a zero-step mdrun. However, I am writing to
> see
> > if anybody knows how reimage based on a selection (would be a single atom
> > in molecule A near the contact between molecule A and B) more elegantly
> > with processing tools available in gromacs.
> >
> > Thank you for your help,
> > Chris.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] temperature coupling groups for homogeneous mixtures/ ionic liquids?

[Kroon, P.C.]

Hi,

yes it matters. In general tc-grps=system is better/correct, unless the
thermal energy transfer across your system is hampered (e.g. a lipid
membrane, or a large protein). It hasn't changed with versions. In
addition, the Berendsen thermostat produces the wrong ensemble.
To check previous simulations, check that the system as a whole, as well as
relevant parts of your simulations display the correct maxwell-boltzmann
distribution of velocities. Even then, there might be some effect which are
hard to quantify.

Peter

On Mon, Jan 16, 2017 at 8:12 PM, Boning Wu 
wrote:

> Dear Gromacs Users,
>
> I am simulating ionic liquids and the mixtures of ionic liquids and neutral
> solvents. I used Berendsen or Nose-Hoover temperature coupling for NPT
> systems. No constrains or restrains are in the system.
>
> I just find these discussions and documentations about the temperature
> coupling groups:
>
> http://www.mail-archive.com/gmx-users@gromacs.org/msg28634.html
>
> http://www.gromacs.org/Documentation/Terminology/Thermostats
>
> I am worried because without realizing the limitations of temperature
> coupling, I used to set my tc groups very arbitrarily in my previous
> simulations, sometimes I use
>
> tc-grps =  CATION ANION NEUTRAL
> and sometimes I use:
>
> tc-grps =  system
>
> Here are my questions:
>
> 1. Of these two grouping methods, which is better for systems
> (a) which is completely homogeneous?
> and (b) which has some nano-domain structures like the aggregations of
> neutral molecules in ionic liquids with size up to 2 nm ( but no phase
> segregation)?
>
> 2. Since now it's almost not possible to re-run all my simulations, does it
> matter if I use two methods arbitrarily? I have attached an mdp file. Most
> work is done by 5.0.4 and 2016.1. How could I check if there is artifact in
> my system?
>
> 3. Since most of the discussions I found are several years ago, did things
> get improved these years? For example, is there anything improved after
> cut-off scheme is replaced by Verlet?
>
> Any help would be appreciated!
>
> Here is my .mdp file
>
> title   =  productrun
> cpp =  /lib/cpp
> define  =
> constraints =  none
> integrator  =  md
> dt  =  0.001; ps !
> nsteps  =  200  ; 2 ns
> nstcomm =  1
> nstxout =  50   ; write x to trr file
> nstvout =  50   ; write v to trr file
> nstxtcout   =  1000 ; write x to xtc file
> nstfout =  0
> nstlog  =  1000 ; write energy to log
> nstenergy   =  1000 ; write energy to edr
> nstlist =  1; frequency to update neighbour list
> ; GPU parameters
> ;verlet-buffer-tolerance  = -1
> ;nstcalclr=  1
> ;nstcalcenergy=  1
> ns_type =  grid
> pbc =  xyz  ; periodic boundry condition
> rlist   =  1.5
> rcoulomb=  1.5
> rvdw=  1.5
> disre   =  simple
> disre-fc=  1000
> coulombtype =  PME
> ; Apply long range dispersion corrections for Energy and Pressure =
> DispCorr=  EnerPres
> ; Spacing for the PME/PPPM FFT grid =
> fourierspacing  = 0.08  ; depends on system
> ; FFT grid size, when a value is 0 fourierspacing will be used =
> fourier_nx  = 0
> fourier_ny  = 0
> fourier_nz  = 0
> ; EWALD/PME/PPPM parameters =
> pme_order= 6
> ewald_rtol   = 1e-05
> ewald_geometry   = 3d
> epsilon_surface  = 0
> optimize_fft = yes
> ; Nose-Hoover temperature coupling is on
> Tcoupl  =  Nose-Hoover
> tc-grps =  system
> tau_t   =  0.2  ; depending on system
> ref_t   =  298.0
> energygrps  =  system
> ; Pressure coupling is on
> Pcoupl  = Parrinello-Rahman
> Pcoupltype  = isotropic
> tau_p   =  1.0; depending on system
> compressibility =  4.5e-5
> ref_p   =  1.0
> gen_vel =  no
> gen_temp=  298.0
> gen_seed  =  43697
>
>
> Thank you,
> Boning Wu
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] MARTINI simulation of protein-protein recognition

[Kroon, P.C.]

@Michael: Yes, you are right, a protein is a protein. IIRC the martinize
script does the same as pdb2gmx in this case.
@James: It really sounds like you want to do DAFT.
http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/downloads/DAFT/index.shtml
seems to contain an tutorial. Otherwise, consider contacting the author of
the paper (T Wassenaar).

Peter

On Mon, Apr 18, 2016 at 3:51 PM, Smith, Micholas D. <smit...@ornl.gov>
wrote:

> Hi James,
>
> My guess is that running a two (unbound) protein simulation with the
> MARTINI force-field will be the same as if it was all atom. Build two
> separate protein topologies (with Martini force-fields) as *.itp files to
> include in your *.top and go from there. The topology file is what grompp
> uses to determine bonding, so if the topology file doesn't have the two
> proteins bound, they won't be. If I remember correctly, you can see an
> example (all-atom) topology file to work with if you use pdb2gmx for a pdb
> that contains 2 chains (with the proper flag the chains will be split).
>
> -Micholas
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of James
> Starlight <jmsstarli...@gmail.com>
> Sent: Monday, April 18, 2016 9:43 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] MARTINI simulation of protein-protein recognition
>
> It seems like smth very complicated :)
>
> I just need to put two different proteins in the system - one in the
> membrane (A) and one in the water (B) and simulate it independently 10
> times to collect statistics about associations of A and B during those
> runs. The problems that I don't know how to put 2 different unbound
> proteins in the MARTINI system.
>
> James
>
> 2016-04-18 9:55 GMT+02:00 Kroon, P.C. <p.c.kr...@rug.nl>:
> > Hi,
> >
> > I assume you want to study the binding of your water soluble protein to
> > your membrane(protein). DAFT was created to do just this. DOI:
> > 10.1021/ct5010092
> >
> > Peter
> >
> > On Fri, Apr 15, 2016 at 3:37 PM, James Starlight <jmsstarli...@gmail.com
> >
> > wrote:
> >
> >> Dear Gromacs users!
> >>
> >> I am looking for some tutorial for the MARTINI simulation of
> >> protein-protein recognition dealing with the big membrane protein
> >> simulated within the membrane and its assosiation with the small water
> >> soluble protein. The question - is it possible in existing Martini
> >> system conisdted of only membrane protein solvated in membrane with
> >> water to
> >> i) increase box size on Z
> >> ii)add some water
> >> iii) put another water soluble protein in new space (on the distance
> >> of the initial membrane protein complex)
> >> iv) edit topology of new system and run new md
> >>
> >> assuming that i,ii and iv are trivial the problem here is the iii step
> :-)
> >>
> >> or alternatively if I would like to run new simulation with those 2
> >> proteins (in the unbound form) how I can prepare such complex system
> >> consisted of big protein in membrane plus water soluble protein
> >> unbound from it?
> >>
> >> Thanks!
> >>
> >> Gleb
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> --
> 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_Lis

Re: [gmx-users] MARTINI simulation of protein-protein recognition

[Kroon, P.C.]

Hi,

I assume you want to study the binding of your water soluble protein to
your membrane(protein). DAFT was created to do just this. DOI:
10.1021/ct5010092

Peter

On Fri, Apr 15, 2016 at 3:37 PM, James Starlight 
wrote:

> Dear Gromacs users!
>
> I am looking for some tutorial for the MARTINI simulation of
> protein-protein recognition dealing with the big membrane protein
> simulated within the membrane and its assosiation with the small water
> soluble protein. The question - is it possible in existing Martini
> system conisdted of only membrane protein solvated in membrane with
> water to
> i) increase box size on Z
> ii)add some water
> iii) put another water soluble protein in new space (on the distance
> of the initial membrane protein complex)
> iv) edit topology of new system and run new md
>
> assuming that i,ii and iv are trivial the problem here is the iii step :-)
>
> or alternatively if I would like to run new simulation with those 2
> proteins (in the unbound form) how I can prepare such complex system
> consisted of big protein in membrane plus water soluble protein
> unbound from it?
>
> Thanks!
>
> Gleb
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] MARTINI crushing

[Kroon, P.C.]

Hmm.. Martini proteins should run fine with ~30fs timesteps. Could you
check the bonded parameters for the bond listed, and take this to the
Martini forum (cgmartini.nl)?
@Mark: The Martini forcefield was validated with timesteps between 10 and
40 fs; although some of the parametrised molecules (such as DNA) only work
with the smaller timesteps.

Peter

On Thu, Apr 14, 2016 at 3:47 PM, James Starlight <jmsstarli...@gmail.com>
wrote:

> actually I have the same system with the same mdp options simulated in
> parallel where I dont have such warnings.  so I dont know the sourse
> of that error in the latter case
>
> the only different between two was t_coupling used in equilibration (0.5
> vs 1.0)
>
> 2016-04-14 15:34 GMT+02:00 Mark Abraham <mark.j.abra...@gmail.com>:
> > Hi,
> >
> > That depends. Why do you think the increase in integration step is a
> valid
> > model physics?
> >
> > Mark
> >
> > On Thu, Apr 14, 2016 at 3:25 PM James Starlight <jmsstarli...@gmail.com>
> > wrote:
> >
> >> another problem when I try to increase slightly integration step from
> >> 0.01 to 0.02 I obtain
> >>
> >> WARNING 1 [file system.top, line 44]:
> >>   The bond in molecule-type Protein_A between atoms 1 BB and 3 BB has an
> >>   estimated oscillational period of 9.7e-02 ps, which is less than 5
> times
> >>   the time step of 2.0e-02 ps.
> >>   Maybe you forgot to change the constraints mdp option.
> >>
> >> that is waht related to constraints in my mdp
> >> constraints  = none
> >> constraint_algorithm = Lincs
> >> unconstrained_start  = no
> >> lincs_order  = 2
> >> lincs_warnangle  = 30
> >>
> >> Can I ignore this warning?
> >>
> >> J.
> >>
> >> 2016-04-14 10:05 GMT+02:00 Kroon, P.C. <p.c.kr...@rug.nl>:
> >> > passing -rdd with a larger value forces mdrun to make larger domain
> >> cells,
> >> > basically reducing the number of ranks you can use and hampering
> >> > parallelization. I don't think it affects the physics.
> >> > Reducing the CPU count does the same thing.
> >> >
> >> > Peter
> >> >
> >> > On Thu, Apr 14, 2016 at 9:57 AM, James Starlight <
> jmsstarli...@gmail.com
> >> >
> >> > wrote:
> >> >
> >> >> an question: might the bigger -rdd like 1.8 or 2.0  produce ssmth bad
> >> >> in simulation? generally I found that with rdd 1.8 the siduation is
> >> >> better, also I reduced number of CPU for that job from 256 to 128 and
> >> >> it works OK by now!
> >> >>
> >> >> Gleb
> >> >>
> >> >> 2016-04-14 9:40 GMT+02:00 Kroon, P.C. <p.c.kr...@rug.nl>:
> >> >> > Hi James,
> >> >> >
> >> >> > 1) use a newer version of Gromacs
> >> >> > 2) try passing -rdd 1.4 or even 1.6 to mdrun. The bonds in Elnedyn
> >> are so
> >> >> > long and flexible they occasionally confuse gromacs' domain
> >> >> decomposition.
> >> >> >
> >> >> > Peter
> >> >> >
> >> >> > On Thu, Apr 14, 2016 at 8:49 AM, James Starlight <
> >> jmsstarli...@gmail.com
> >> >> >
> >> >> > wrote:
> >> >> >
> >> >> >> Dear Gromacs Users!
> >> >> >>
> >> >> >> I faced with the problems while simulating of big MARTINI system
> of
> >> >> >> membrane protein complex within big membrane consisted totally of
> 55k
> >> >> >> martini CG atoms.
> >> >> >>
> >> >> >> On the early stage of the NPT equilibration I have a error
> >> >> >>
> >> >> >> Program g_mdrun_openmpi, VERSION 4.5.7
> >> >> >> Source code file:
> >> >> >> /builddir/build/BUILD/gromacs-4.5.7/src/mdlib/domdec_top.c, line:
> 173
> >> >> >>
> >> >> >> Software inconsistency error:
> >> >> >> Some interactions seem to be assigned multiple times
> >> >> >> For more information and tips for troubleshooting, please check
> the
> >> >> GROMACS
> >> >> >> website at http://www.gromacs.org/Documentation/Errors
> >> >> >> ---
> &g

Re: [gmx-users] MARTINI crushing

[Kroon, P.C.]

passing -rdd with a larger value forces mdrun to make larger domain cells,
basically reducing the number of ranks you can use and hampering
parallelization. I don't think it affects the physics.
Reducing the CPU count does the same thing.

Peter

On Thu, Apr 14, 2016 at 9:57 AM, James Starlight <jmsstarli...@gmail.com>
wrote:

> an question: might the bigger -rdd like 1.8 or 2.0  produce ssmth bad
> in simulation? generally I found that with rdd 1.8 the siduation is
> better, also I reduced number of CPU for that job from 256 to 128 and
> it works OK by now!
>
> Gleb
>
> 2016-04-14 9:40 GMT+02:00 Kroon, P.C. <p.c.kr...@rug.nl>:
> > Hi James,
> >
> > 1) use a newer version of Gromacs
> > 2) try passing -rdd 1.4 or even 1.6 to mdrun. The bonds in Elnedyn are so
> > long and flexible they occasionally confuse gromacs' domain
> decomposition.
> >
> > Peter
> >
> > On Thu, Apr 14, 2016 at 8:49 AM, James Starlight <jmsstarli...@gmail.com
> >
> > wrote:
> >
> >> Dear Gromacs Users!
> >>
> >> I faced with the problems while simulating of big MARTINI system of
> >> membrane protein complex within big membrane consisted totally of 55k
> >> martini CG atoms.
> >>
> >> On the early stage of the NPT equilibration I have a error
> >>
> >> Program g_mdrun_openmpi, VERSION 4.5.7
> >> Source code file:
> >> /builddir/build/BUILD/gromacs-4.5.7/src/mdlib/domdec_top.c, line: 173
> >>
> >> Software inconsistency error:
> >> Some interactions seem to be assigned multiple times
> >> For more information and tips for troubleshooting, please check the
> GROMACS
> >> website at http://www.gromacs.org/Documentation/Errors
> >> ---
> >>
> >>
> >> does the problem is related to paralelization or smth wrong with
> >> setup? Amazing that on the same system without Elnedyn applied I have
> >> no such promlems at ell.
> >>
> >> Thanks so much for help!
> >>
> >> J.
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] MARTINI crushing

[Kroon, P.C.]

Hi James,

1) use a newer version of Gromacs
2) try passing -rdd 1.4 or even 1.6 to mdrun. The bonds in Elnedyn are so
long and flexible they occasionally confuse gromacs' domain decomposition.

Peter

On Thu, Apr 14, 2016 at 8:49 AM, James Starlight 
wrote:

> Dear Gromacs Users!
>
> I faced with the problems while simulating of big MARTINI system of
> membrane protein complex within big membrane consisted totally of 55k
> martini CG atoms.
>
> On the early stage of the NPT equilibration I have a error
>
> Program g_mdrun_openmpi, VERSION 4.5.7
> Source code file:
> /builddir/build/BUILD/gromacs-4.5.7/src/mdlib/domdec_top.c, line: 173
>
> Software inconsistency error:
> Some interactions seem to be assigned multiple times
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
>
> does the problem is related to paralelization or smth wrong with
> setup? Amazing that on the same system without Elnedyn applied I have
> no such promlems at ell.
>
> Thanks so much for help!
>
> J.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Question for Gromacs Users

[Kroon, P.C.]

This is a known bug in Martinize; you applied the correct fix.
And Justin is right, it would have been better to post this kind of
question on the Martini forum (www.cgmartini.nl); I'm also rather sure that
this answer is on there somewhere.

Peter

On Tue, Apr 12, 2016 at 8:43 PM, Justin Lemkul  wrote:

>
>
> On 4/12/16 2:22 PM, Brier, Troy wrote:
>
>> To whom it may concern,
>>
>> I am attempting to run a single protein in water Martini coarse grain
>> simulation. I used martinize.py (version 2.4) to coarse grain the
>> protein and add a dilsulfide bond. When attempting to run the
>> minimization phase (I am using Gromacs version 5.1) I receive the
>> following error:
>>
>> Fatal error:
>> Incorrect number of parameters - found 1, expected 2 or 4 for Bond.For
>> more information and tips for troubleshooting, please check the
>> GROMACS website at http://www.gromacs.org/Documentation/Errors
>>
>> After troubleshooting I determined the error came from the Bonds
>> section in the Protein_A.itp file produced from martinize.py, and
>> specifically from the section having to do with the disulfide bonds.
>> The error seems to be related to martinize.py determining the bond
>> constraints of the disulfide bone to not match those of the literature
>> values, and the script prints the following message:
>>
>> Note: Cysteine bonds are 0.24 nm constraints, instead of the published
>> 0.39nm/5000kJ/mol.
>>
>> So I changed the section in the Protein_A.itp file from:
>>
>> (Error Causing  Protein_A.itp file under [bonds])
>> ; Links/Cystine bridges
>>253   281  1   0.24000
>>
>> to:
>>
>>   (Error Causing  Protein_A.itp file under [bonds])
>> ; Links/Cystine bridges
>>253   281  1   0.39000 5000
>>
>>
>> and then the minimization step runs without the fatal error. What I
>> would like to know if making this change is the proper thing to do or
>> should I keep the constraint distance at 0.24 nm and just add in the
>> bond strength of 5000 kJ/mol?
>>
>>
> The wording of the error message states that it's supposed to be a
> constraint (i.e. fixed distance), not a harmonic interaction.  So if it's a
> constraint, it's simply being written to the wrong section of the
> topology.  It may be better to post this question to the MARTINI forum.  A
> difference between a rigid 0.24 nm distance and a harmonic 0.39 nm distance
> is quite substantial.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Problem compiling Gromacs 5.1

[Kroon, P.C.]

Just use your favourite text editor.

Peter

On Thu, Aug 20, 2015 at 3:10 AM, atsutoshi0...@gmail.com wrote:

 Line 52 of cmake/FindSphinx.cmake file is written below.
 string(REGEX REPLACE Sphinx \\([^)]*\\) ([^ ]+) \\1
 SPHINX_EXECUTABLE_VERSION ${SPHINX_VERSION_OUTPUT_VARIABLE})

 Can you tell me how I can change the line?

 Bests,
 Leucer


 2015/08/19 23:11、Mark Abraham mark.j.abra...@gmail.com のメッセージ:

  Hi,
  On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 atsutoshi0...@gmail.com wrote:
 
  Hi,
 
  I am unable to  compile Gromamcs 5.1 using the following cmake command.
  cmake .. -DGMX_FFT_LIBRARY=fftpack
  -DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off
  -DGMX_THREAD_MPI=off -DGMX_MPI=on -DGMX_CPU_ACCELERATION=SSE4.1
 
 
  Unrelated, but you now need to use -DGMX_SIMD=SSE4.1 to have the same
  effect.
 
 
  -DGMX_USE_RDTSCP=off
 
  Then I got the error message.
  Boost = 1.44 not found. Using minimal internal version. This may cause
  trouble if you plan on compiling/linking other software that uses Boost
  against GROMACS.
  CMake Error at cmake/FindSphinx.cmake:52 (string):
   string sub-command REGEX, mode REPLACE needs at least 6 arguments total
  to
   command.
  Call Stack (most recent call first):
   docs/CMakeLists.txt:62 (find_package)
 
  Could you advice what could be causing this error?
 
  We try to find Sphinx in case people want to build the new documentation,
  but it looks like some part of the detection isn't reliable enough. Can
 you
  please try changing line 52 of cmake/FindSphinx.cmake to read
 
 string(REGEX REPLACE Sphinx \\([^)]*\\) ([^ ]+) \\1
  SPHINX_EXECUTABLE_VERSION ${SPHINX_VERSION_OUTPUT_VARIABLE})
 
  and let us know how you go?
 
  Mark
 
  I was able to compile Gromacs 5.0 using same cmake command….
 
  Bests,
  Leucer
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
  posting!
 
  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
  * For (un)subscribe requests visit
  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
  send a mail to gmx-users-requ...@gromacs.org.
  --
  Gromacs Users mailing list
 
  * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!
 
  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
  * For (un)subscribe requests visit
  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.
 --
 Gromacs Users mailing list

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

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

 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.

-- 
Gromacs Users mailing list

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

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.