Re: [gmx-users] mail about installation og gromacs 4.6.1

[Mark Abraham]

Hi,

If you feel you must install software that is three years old and no longer
supported, please at least get the latest bug-fix version of it (4.6.7).
You should consider carefully one of the more recent, faster and less buggy
versions.

I can't tell what your problem is, but my guess is that you are installing
as root, which is a bad idea. Follow the install guides, which make clear
that you only need root privileges for the final "make install" step.

Mark

On Sat, Oct 1, 2016 at 3:29 PM subramanian vidhyasankar 
wrote:

> Respected justin
>  Thank you for your previous reply
> I would like to install gromacs 4.6.1 single precession for some reason
> when i use the following command
> cmake .. -DGMX_BUILD_OWN_FFTW=ON   -DCMAKE_INSTALL_PREFIX=/opt/gromacs
>
> it sucessfully configures
>
> But when i* complile using make command *
>
> it shows error as follows
>
>
>
>
>
>
>
>
>
>
> *CMake Error at gpu_utils_generated_memtestG80_core.cu.o.Release.cmake:207
> (message):  Error generating
>
> /root/gromacs-4.6.7/build/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.omake[2]:
> ***
>
> [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/gpu_utils_generated_memtestG80_core.cu.o]
> Error 1make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all]
> Error 2make: *** [all] Error 2*
>
>
>
> *plase help me to install single precession *
>
> *with high regards*
>
> *S.Vidhyasankar*
> --
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[gmx-users] segmentation fault in md

[ISHRAT JAHAN]

Dear all
 I am trying to simulate 3M urea in a water box.when i do the mdrun of pr ,
i get too many LINCS warning and also segmentation fault(core dumped).

I am pasting my em.mdp and pr.mdp file below-
em.mdp
;
;User spoel (236)
;Wed Nov  3 17:12:44 1993
;Input file
;
cpp =  /usr/bin/cpp
define  =  -DFLEX_SPC
constraints = all-bonds
integrator  = steep
nsteps  =  2000
;
;Energy minimizing stuff
;
emtol   =  100
emstep  =  0.01
nstcomm =  1
ns_type =  grid
rlist   =  0.15
coulombtype = PME
rcoulomb=  0.15
rvdw= .19
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no


pr.mdp

;
;User spoel (236)
;Wed Nov  3 17:12:44 1993
;Input file
;
title   =  Yo
cpp =  /usr/bin/cpp
define  =  -DPOSRES
constraints = all-bonds
constraintalgorithm =  LINCS
integrator  =  md
dt  =  0.001; ps !
nsteps  =  1; total 50 ps.
nstcomm =  10
nstxout =  500
nstvout =  1000
nstfout = 10
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  2
coulombtype =  PME
rcoulomb=  2
rvdw=  2
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl  =  V-rescale
tc-grps=  URE   Water
tau_t   =  0.10.1
ref_t   =  300300
; Energy monitoring
energygrps=  URE Water
; Pressure coupling is on
Pcoupl  =  Berendsen
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529

thanks in advance
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Re: [gmx-users] restarting the crashed run

[Mark Abraham]

Hi,

The default name for that file is confout.gro, which it will be unless you
chose a different name with

gmx mdrun -c nvt.gro

or

gmx mdrun -deffnm nvt

However, you can sometimes
get slightly better results by using

gmx grompp -c whatever -p topol -t nvt.cpt -f npt -o npt

because now the box, coordinates and velocities are read at full precision
from the nvt checkpoint, unlike when you read the npt gro file.

Mark

On Mon, Oct 3, 2016 at 5:39 AM Roshan Shrestha  wrote:

> I had restarted my crash run for NVT equilibration using* gmx mdrun -s
> nvt.tpr -cpi nvt.cpt -v *, the simulation restarted and finished fine, but
> at the end of the simulation I did not get my nvt.gro, which I needed to do
> further NPT equilibration. Where is nvt.gro ? Did I do something wrong, or
> the file has been renamed to something ? Please suggest me. Thanks
>
>
> --
> Roshan Shrestha
> Graduate Student
> Central Department of Physics,Tribhuvan University
> Kathmandu,Nepal
> --
> Gromacs Users mailing list
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Re: [gmx-users] gromacs mdrun problem

[Mark Abraham]

Hi,

The list does not accept attachments, unfortunately. However, your problem
is probably solvable via the advice at
http://www.gromacs.org/Documentation/Terminology/Blowing_Up. There's also
probably no reason to do a run with position restraints for urea in water,
since there's little that is special about your starting configuration. See
also http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents.

Mark

On Mon, Oct 3, 2016 at 8:25 AM ISHRAT JAHAN  wrote:

> Dear all
>  I am trying to simulate 3M urea in a water box.when i do the mdrun of pr ,
> i get too many LINCS warning and also segmentation fault(core dumped).
>
> I am attaching my em.mdp and pr.mdp file below-
>
>
>
>
>
>
> Thanks in advance
> --
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> posting!
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[gmx-users] gromacs mdrun problem

[ISHRAT JAHAN]

Dear all
 I am trying to simulate 3M urea in a water box.when i do the mdrun of pr ,
i get too many LINCS warning and also segmentation fault(core dumped).

I am attaching my em.mdp and pr.mdp file below-






Thanks in advance
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[gmx-users] restarting the crashed run

[Roshan Shrestha]

I had restarted my crash run for NVT equilibration using* gmx mdrun -s
nvt.tpr -cpi nvt.cpt -v *, the simulation restarted and finished fine, but
at the end of the simulation I did not get my nvt.gro, which I needed to do
further NPT equilibration. Where is nvt.gro ? Did I do something wrong, or
the file has been renamed to something ? Please suggest me. Thanks


-- 
Roshan Shrestha
Graduate Student
Central Department of Physics,Tribhuvan University
Kathmandu,Nepal
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[gmx-users] moleculaes breaking off after EM - help

[Thejus Kartha]

Greetings!
I was performing an EM run with an array of dioxane molecules, for which I had 
produced co-ordinates from PRODRG. I got the co-ordinates, and made an array of 
it, using the gmx genconf module, and corrected my topology file. Then, I 
thought I should minimize the energy of this array before solvating it, or 
anything. So, as I was running the grompp module using mdp files from Dr. 
Lemkul's tutorials, it gave me the following error:
Steepest Descents converged to machine precision in 641 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  2.6059185e+09
Maximum force =  8.6477500e+04 on atom 557
Norm of force =  7.7685435e+03

I am presuming there's something seriously wrong with my input files, as I've 
been told many times before. That said, how do I tweak around with my mdp file 
in this case? I mean, there's this Fmax value that I have to deal with. How do 
I know if I am using the right threshold for Fmax? Do I base this value on 
information from literature? And of course, when I open the .gro file after the 
EM, I find my molecules to be smashed to smithereens. There are points and 
broken triangles flying around in all directions (dioxane is a hexagon, and it 
has broken to half.) Why does this happen? Please help me.
Thanks & Regards,Thejus R. KarthaM.Sc. ChemistryCentral University of Tamil Nadu
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Re: [gmx-users] energy minimisation - LINCS WARNING

[Justin Lemkul]

Please don't reply to digests or unrelated threads when starting a new topic; it 
creates a mess in the archive.


On 10/2/16 6:11 PM, Nash, Anthony wrote:

Hi all,

I had a homology/de-novo model .pdb converted into .gro, solvated,
neutralised and now I¹m going through a series of energy minimisation
steps. Unfortunately, during energy minimisation I get LINCS WARNINGS
(angle relative constraint deviation). The the naked eye, the atoms
involved don¹t look untoward.


When I used LINCS all-bond I get the following error:
---

Step -1, time -0.001 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001657, max 0.033500 (between atoms 1362 and 1363)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length



When I reduced this to only be the hydrogen bonds (h-bonds) I get:
---
Step 20, time 0.02 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.00, max 0.00 (between atoms 1322 and 1324)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1360   1361   37.50.1010   0.1010  0.1010
[continues with more errors until Segmentation fault 11]


I have tried both constraints with a reduced and increased deltaStep
(0.2,0.02,0.002,0.0002) no change. I have also taken constraints off, this
does work but then fails again when constraints are returned. I have tried
both Steep and cg, both fail with the same result.

The .mdp file I used (taken from the latest release of Justin¹s tutorials)
is:
; energy.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 700.0; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep  = 0.002  ; Energy step size
nsteps  = 20; Maximum number of (minimization)
steps to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
cutoff_scheme = verlet
nstlist = 20; Frequency to update the neighbor list
and long range forces
ns_type = grid  ; Method to determine neighbor list
(simple, grid)
rlist   = 1.4   ; Cut-off for making neighbor list (short
range forces)
coulombtype = PME   ; Treatment of long range electrostatic
interactions
rcoulomb= 1.4   ; Short-range electrostatic cut-off
rvdw= 1.4   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)

;ADDED THIS BIT MYSELF
continuation= no   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = h-bonds; all-bonds (even heavy atom-H bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 8 ; also related to accuracy


The .pdb was generated using I-TASSER. I have tried refining the hydrogen
placement via -ignh during pdb2gmx, and I also tried ³Protein Preparation²
(bond ordering - again, hydrogen bond placement) in Schrodinger. All the
same.

I was hoping that I could actually watch a rough-and-ready minimisation
using Avogadro, however, the release I have keeps crashing whilst trying
to open large structures.

Any suggestions on what I could try next?



All signs point to unreasonable starting structure.  How about minimizing the 
protein alone, in vacuo?  Maybe restrain the backbone and try to minimize side 
chains, then in the absence of any restraints?


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] energy minimisation - LINCS WARNING

[Nash, Anthony]

Hi all,

I had a homology/de-novo model .pdb converted into .gro, solvated,
neutralised and now I¹m going through a series of energy minimisation
steps. Unfortunately, during energy minimisation I get LINCS WARNINGS
(angle relative constraint deviation). The the naked eye, the atoms
involved don¹t look untoward.


When I used LINCS all-bond I get the following error:
---

Step -1, time -0.001 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001657, max 0.033500 (between atoms 1362 and 1363)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length



When I reduced this to only be the hydrogen bonds (h-bonds) I get:
---
Step 20, time 0.02 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.00, max 0.00 (between atoms 1322 and 1324)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1360   1361   37.50.1010   0.1010  0.1010
[continues with more errors until Segmentation fault 11]


I have tried both constraints with a reduced and increased deltaStep
(0.2,0.02,0.002,0.0002) no change. I have also taken constraints off, this
does work but then fails again when constraints are returned. I have tried
both Steep and cg, both fail with the same result.

The .mdp file I used (taken from the latest release of Justin¹s tutorials)
is:
; energy.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 700.0; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep  = 0.002  ; Energy step size
nsteps  = 20; Maximum number of (minimization)
steps to perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
cutoff_scheme = verlet
nstlist = 20; Frequency to update the neighbor list
and long range forces
ns_type = grid  ; Method to determine neighbor list
(simple, grid)
rlist   = 1.4   ; Cut-off for making neighbor list (short
range forces)
coulombtype = PME   ; Treatment of long range electrostatic
interactions
rcoulomb= 1.4   ; Short-range electrostatic cut-off
rvdw= 1.4   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)

;ADDED THIS BIT MYSELF
continuation= no   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = h-bonds; all-bonds (even heavy atom-H bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 8 ; also related to accuracy


The .pdb was generated using I-TASSER. I have tried refining the hydrogen
placement via -ignh during pdb2gmx, and I also tried ³Protein Preparation²
(bond ordering - again, hydrogen bond placement) in Schrodinger. All the
same. 
 
I was hoping that I could actually watch a rough-and-ready minimisation
using Avogadro, however, the release I have keeps crashing whilst trying
to open large structures.

Any suggestions on what I could try next?


Thanks
Anthony

Dr Anthony Nash
Department of Chemistry
University College London

Skeletal Tissue Dynamics Group
Committee member of London Matrix Group @LondonMatrixGrp





On 02/10/2016 19:06, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Karel de Vries"
 wrote:

>Mark,
>
>I understand your concern.
>I need to have the hydrogens for my final answer, so an all-atom force
>field is definitely inevitable. Justification for choosing OPLS over the
>other all-atom force fields is a little more tricky, but I have found
>literature where they used OPLS-aa for similar purposes so I figured it
>should work. As for the presence of a quaternary carbon, I expect that to
>be the "alkane C", opls_139. Given that opls_135 through 138 are "alkane
>CHn", this sounds like the most reasonable interpretation of opls_139.
>
>I will try to find better documentation for the exact meaning of these
>atom
>types though, thanks.
>
>On Fri, Sep 30, 2016 at 1:49 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 9/30/16 7:14 AM, Karel de Vries wrote:
>>
>>> Hi Justin,
>>>
>>> Thanks for your answer; I assumed that TopolGen is not intentionally
>>> incorrect. What I meant to ask was whether it was intentionally
>>>different
>>> from what the comments in the atomtypes.atp file indicate. I thought
>>>that
>>> perhaps, based on past experience, you know that some choices work
>>>better
>>> than others and included this into your script. I would not want to
>>>undo
>>> this by cooking up my own assignments based on no past experience at
>>>all.
>>>
>>>
>> Nope, it's just based on the normal principal of trying to 

Re: [gmx-users] Simulating PMMA

[Karel de Vries]

Mark,

I understand your concern.
I need to have the hydrogens for my final answer, so an all-atom force
field is definitely inevitable. Justification for choosing OPLS over the
other all-atom force fields is a little more tricky, but I have found
literature where they used OPLS-aa for similar purposes so I figured it
should work. As for the presence of a quaternary carbon, I expect that to
be the "alkane C", opls_139. Given that opls_135 through 138 are "alkane
CHn", this sounds like the most reasonable interpretation of opls_139.

I will try to find better documentation for the exact meaning of these atom
types though, thanks.

On Fri, Sep 30, 2016 at 1:49 PM, Justin Lemkul  wrote:

>
>
> On 9/30/16 7:14 AM, Karel de Vries wrote:
>
>> Hi Justin,
>>
>> Thanks for your answer; I assumed that TopolGen is not intentionally
>> incorrect. What I meant to ask was whether it was intentionally different
>> from what the comments in the atomtypes.atp file indicate. I thought that
>> perhaps, based on past experience, you know that some choices work better
>> than others and included this into your script. I would not want to undo
>> this by cooking up my own assignments based on no past experience at all.
>>
>>
> Nope, it's just based on the normal principal of trying to construct
> additive force fields from building blocks.  Take what's known, assign a
> best match, otherwise default to some stock parameter, then clearly warn
> the user that the script can be dangerous :)
>
> -Justin
>
>
> Karel
>>
>> On Fri, Sep 30, 2016 at 12:00 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 9/30/16 3:35 AM, Karel de Vries wrote:
>>>
>>> Hi again,

 I think the problem is in the force field description that I put in the
 aminoacids.rtp file. Like I said, I just got the output from Justin's
 TopolGen (V1.1) script. Upon comparison of the opls_xxx choices to the
 comments in the atomtypes.atp file, a few strange assignments turn up.
 For
 example, the Os are taken to be from the C=O in an amide. However, there
 is
 no nitrogen in PMMA at all. There is a C=O in PMMA, but it's an ester
 group. There are a few more doubtful choices, e.g. a C bound to four
 other
 Cs is assigned the "alkane CH3" atom.

 I have two questions.
 One concerns the TopolGen script: are these seemingly incorrect
 assignments
 intentional? Or is this just a limitation in the script? There is
 another
 TopolGen topology for PMMA online, at
 http://gromacs-oplsaa-topologies.wikia.com/wiki/PMMA_3-mer, which has
 slightly different but similarly doubtful assignments.


 I would never write a program that is intentionally incorrect.  TopolGen
>>> tries to guess the best parameter based on connectivity, and sometimes it
>>> guesses wrong, because it is pretty much impossible to design a script
>>> that
>>> will account for the vast chemical space that OPLS-AA encompasses.  I try
>>> to make this abundantly clear in the final message printed to the screen
>>> by
>>> TopolGen:
>>>
>>> "Output topology has been written. An attempt has been made to assign
>>> charges and atom types based on existing functional groups, but they may
>>> not be correct.  No charge calculations or other parameterization
>>> calculations have been done. Guesses have been made for charge groups.
>>> Please inspect and correct the topology before using it in any
>>> simulations.  The author of the script does NOT guarantee accuracy or
>>> usability of any of the content; TopolGen was written as a convenience
>>> for
>>> outputting a skeleton topology, and nothing more."
>>>
>>> -Justin
>>>
>>>
>>> The second is about the opls-aa force field. Is there any other
>>>
 documentation on which assignments to make than just the comments in the
 atomtypes.atp file?


 Regarding Chaofu Wu's reply to my original email; thank you very much
 for
 your comments. I accidentally sent a template file, not one used for an
 actual run. I run gromacs with lower nst* values; when I need
 statistics I
 make sure there are about 1000 frames in the energy file. Values I
 adjust
 from the parameters I sent are nsteps, nst*, ref_t, ref_p, and for the
 initial run also gen_vel / gen_temp. I'm sorry for the confusion.

 Karel de Vries


 On Wed, Sep 28, 2016 at 11:43 AM, Karel de Vries 
 wrote:

 Hello all,

>
> I'm trying to simulate bulk PMMA, poly(methyl methacrylate) in Gromacs.
> I'm using the opls-aa force field. I added a PMMA unit cell to the
> aminoacids.rtp file (listing below). I'm running a simulation with 30
> molecules of 50 unit cells each. I start by putting straight strands
> into
> the box with gmx insert-molecules.
>
> I think that my input parameters are incorrect. My first reason for
> thinking this is that it is very difficult to equilibrate this system:
> it
> takes a lo

Re: [gmx-users] g_membed failure

[Mark Abraham]

Hi,

Did you start with
http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-features.html#running-a-membrane-protein-embedding-simulation?


Mark

On Sun, 2 Oct 2016 17:13 Sophia Kuriakidi  wrote:

> Hi again to all of you!
> I am trying to run at last this membrane simulation. I am trying to use the
> -membed option but I can't figure out how to. Can anyone provide me with an
> example input line? e.g. gmx mdrun -membed -input file -n index.ndx -p
> topol.top -o output file etc ? And also, can anyone provide with an example
> embed.dat? Thanks a lot in advance!
>
> 2016-09-22 10:38 GMT+03:00 Sophia Kuriakidi :
>
> > Thank you so much Tom, I will try that!
> >
> > 2016-09-21 21:11 GMT+03:00 Thomas Piggot :
> >
> >> g_membed is now part of mdrun, so you would need to use mdrun with the
> >> -membed option. From mdrun -h:
> >>
> >> /"The option -membed does what used to be g_membed, i.e. embed a protein
> >> into a//
> >> //membrane. This module requires a number of settings that are provided
> >> in a//
> >> //data file that is the argument of this option. For more details in
> >> membrane//
> >> //embedding, see the documentation in the user guide. The options -mn
> and
> >> -mp//
> >> //are used to provide the index and topology files used for the
> >> embedding."/
> >>
> >> Cheers
> >>
> >> Tom
> >>
> >>
> >> On 21/09/16 18:36, Sophia Kuriakidi wrote:
> >>
> >>> Thank you for your responses!
> >>>
> >>> Sotirios:"Also the way this worked for me was to use an index file. I
> >>> made
> >>> an index of the prot + lig + crystallographic waters and I used it in
> >>> both
> >>> grompp and g_membed. In the latter I just used the group and then
> >>> selected
> >>> the POPC. You must also include the group's name in the mdp in order
> for
> >>> it
> >>> to work."
> >>> I also have grouped the ligand with the protein (but not any waters)
> and
> >>> I
> >>> included the index in the mdp file.
> >>>
> >>> Thomas:"My guess is that you probably also have an older version of the
> >>> g_membed program installed on your system and as you are trying to use
> a
> >>> more recent tpr (from version 5.1.2), this might be what is causing the
> >>> segmentation fault. That said, if I try a tpr from GROMACS 5.0.6 with
> >>> g_membed 4.5.7 it does give me a warning about a mismatch of versions
> so
> >>> I
> >>> could be wrong (but what you say you are doing shouldn't be possible)."
> >>>
> >>> It seems that this is the case because I am using 5.1.2. How could I
> >>> resolve this problem? How coould I use g_membed in 5.1.2? Or how I
> could
> >>> alternatively insert my protein into a membrane bilayer?
> >>>
> >>> Thanks again!
> >>>
> >>>
> >>>
> >>> 2016-09-14 13:47 GMT+03:00 Thomas Piggot :
> >>>
> >>> Hi,
> 
>  In more recent versions of GROMACS (4.6.x and above IIRC), the
> g_membed
>  feature is only available using mdrun (see mdrun -h) and so the
> g_membed
>  command should either no longer work at all or print you a note to
> tell
>  you
>  to use mdrun (depending upon version).
> 
>  My guess is that you probably also have an older version of the
> g_membed
>  program installed on your system and as you are trying to use a more
>  recent
>  tpr (from version 5.1.2), this might be what is causing the
> segmentation
>  fault. That said, if I try a tpr from GROMACS 5.0.6 with g_membed
> 4.5.7
>  it
>  does give me a warning about a mismatch of versions so I could be
> wrong
>  (but what you say you are doing shouldn't be possible).
> 
>  Cheers
> 
>  Tom
> 
> 
>  On 14/09/16 08:40, Sotirios Dionysios I. Papadatos wrote:
> 
>  Hi, run some diagnostics, don't use the -xyinit etc
> >
> > Try the basics gmx g_membed -f -p ... etc
> >
> > Also the way this worked for me was to use an index file. I made an
> > index
> > of the prot + lig + crystallographic waters and I used it in both
> > grompp
> > and g_membed. In the latter I just used the
> >
> > group and then selected the POPC. You must also include the group's
> > name
> > in the mdp in order for it to work.
> >
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of
> Sophia
> > Kuriakidi 
> > Sent: Tuesday, September 13, 2016 9:18:12 PM
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] g_membed failure
> >
> > Hi all,
> > I am trying to use g_membed in order to embed my protein in a lipid
> > bilayer
> > (I am using dppc). I am using the tutorial of Appendix A of this
> paper:
> >
> > *http://wwwuser.gwdg.de/~ggroenh/submitted/Membed_rev.pdf
> > *
> >
> > I am creating  an input.tpr using this command:
> >
> > grompp -f sample.mdp -c merged.gro 

Re: [gmx-users] g_membed failure

[Sophia Kuriakidi]

Hi again to all of you!
I am trying to run at last this membrane simulation. I am trying to use the
-membed option but I can't figure out how to. Can anyone provide me with an
example input line? e.g. gmx mdrun -membed -input file -n index.ndx -p
topol.top -o output file etc ? And also, can anyone provide with an example
embed.dat? Thanks a lot in advance!

2016-09-22 10:38 GMT+03:00 Sophia Kuriakidi :

> Thank you so much Tom, I will try that!
>
> 2016-09-21 21:11 GMT+03:00 Thomas Piggot :
>
>> g_membed is now part of mdrun, so you would need to use mdrun with the
>> -membed option. From mdrun -h:
>>
>> /"The option -membed does what used to be g_membed, i.e. embed a protein
>> into a//
>> //membrane. This module requires a number of settings that are provided
>> in a//
>> //data file that is the argument of this option. For more details in
>> membrane//
>> //embedding, see the documentation in the user guide. The options -mn and
>> -mp//
>> //are used to provide the index and topology files used for the
>> embedding."/
>>
>> Cheers
>>
>> Tom
>>
>>
>> On 21/09/16 18:36, Sophia Kuriakidi wrote:
>>
>>> Thank you for your responses!
>>>
>>> Sotirios:"Also the way this worked for me was to use an index file. I
>>> made
>>> an index of the prot + lig + crystallographic waters and I used it in
>>> both
>>> grompp and g_membed. In the latter I just used the group and then
>>> selected
>>> the POPC. You must also include the group's name in the mdp in order for
>>> it
>>> to work."
>>> I also have grouped the ligand with the protein (but not any waters) and
>>> I
>>> included the index in the mdp file.
>>>
>>> Thomas:"My guess is that you probably also have an older version of the
>>> g_membed program installed on your system and as you are trying to use a
>>> more recent tpr (from version 5.1.2), this might be what is causing the
>>> segmentation fault. That said, if I try a tpr from GROMACS 5.0.6 with
>>> g_membed 4.5.7 it does give me a warning about a mismatch of versions so
>>> I
>>> could be wrong (but what you say you are doing shouldn't be possible)."
>>>
>>> It seems that this is the case because I am using 5.1.2. How could I
>>> resolve this problem? How coould I use g_membed in 5.1.2? Or how I could
>>> alternatively insert my protein into a membrane bilayer?
>>>
>>> Thanks again!
>>>
>>>
>>>
>>> 2016-09-14 13:47 GMT+03:00 Thomas Piggot :
>>>
>>> Hi,

 In more recent versions of GROMACS (4.6.x and above IIRC), the g_membed
 feature is only available using mdrun (see mdrun -h) and so the g_membed
 command should either no longer work at all or print you a note to tell
 you
 to use mdrun (depending upon version).

 My guess is that you probably also have an older version of the g_membed
 program installed on your system and as you are trying to use a more
 recent
 tpr (from version 5.1.2), this might be what is causing the segmentation
 fault. That said, if I try a tpr from GROMACS 5.0.6 with g_membed 4.5.7
 it
 does give me a warning about a mismatch of versions so I could be wrong
 (but what you say you are doing shouldn't be possible).

 Cheers

 Tom


 On 14/09/16 08:40, Sotirios Dionysios I. Papadatos wrote:

 Hi, run some diagnostics, don't use the -xyinit etc
>
> Try the basics gmx g_membed -f -p ... etc
>
> Also the way this worked for me was to use an index file. I made an
> index
> of the prot + lig + crystallographic waters and I used it in both
> grompp
> and g_membed. In the latter I just used the
>
> group and then selected the POPC. You must also include the group's
> name
> in the mdp in order for it to work.
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sophia
> Kuriakidi 
> Sent: Tuesday, September 13, 2016 9:18:12 PM
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] g_membed failure
>
> Hi all,
> I am trying to use g_membed in order to embed my protein in a lipid
> bilayer
> (I am using dppc). I am using the tutorial of Appendix A of this paper:
>
> *http://wwwuser.gwdg.de/~ggroenh/submitted/Membed_rev.pdf
> *
>
> I am creating  an input.tpr using this command:
>
> grompp -f sample.mdp -c merged.gro -p merged.top -o input.tpr
>
> and it works fine. Then when I am trying to use g_membed by typping
> this:
>
> g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000
>
>or this
>
>g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000
> -zinit 1.1 -zend 1.0 -nz 100
>
> I just get the g_membed manual printed out...
>
> $ g_membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000