Re: [gmx-users] No convergence with g_nmeig

[KARAKAS Esra]

Dear gromacs users,

I still have the same problem with the vector convergence. There is a link with 
the size of my protein (18 081 atoms) ?
I tried with a small molecule composed with 826 atoms and it seems to work.

Any idea, please.

Best

Esra





Hi,

Thank you for your response. I used a supercomputer and all tools are compiled 
with mpi, I used 1 cpu and I have
also the same result.

Best,

Esra

Message: 2
Date: Thu, 5 Nov 2015 14:45:27 +
From: Joaquim Rui de Castro Rodrigues 
>
To: 
"gmx-users@..."
 
>
Subject: Re: [gmx-users] No convergence with g_nmeig
Message-ID:

<99DCD30D03D1124CBDFCE15D7659B63183F0AA9A75@...>
Content-Type: text/plain; charset="us-ascii"

Hi,

You seem to be running the calculation in parallel (g_nmeig_mpi_d). I don't 
think this is possible. Have
you tried the nmeig serial version?

HTH,
Rui Rodrigues


De: 
gromacs.org_gmx-users-bounces@...
[gromacs.org_gmx-users-bounces@...]
 Em Nome De
KARAKAS Esra 
[Esra.Karakas@...]
Enviado: quinta-feira, 5 de Novembro de 2015 11:08
Para: 
gromacs.org_gmx-users@...
Assunto: Re: [gmx-users] No convergence with g_nmeig

Any idea, please.

Best

Esra KARAKAS

Dear gromacs users,

I am trying to diagonalize my Hessian matrix obtained from mdrun (normal mode
calulation) but I have this message and my vector 1 doesn't converge :

GROMACS:  gmx nmeig, VERSION 5.0.4 (double precision)
Executable:   /usr/local/gromacs-5.0.4/bin/gmx_mpi_d
Library dir:  /usr/local/gromacs-5.0.4/share/gromacs/top
Command line:
  g_nmeig_mpi_d -s nm.tpr -f nm.mtx -v eigenvec_TEST -of eigenfreq_TEST -ol
eigenval_TEST

Reading file nm.tpr, VERSION 5.0.4 (double precision)
Reading file nm.tpr, VERSION 5.0.4 (double precision)
Reading double precision matrix generated by Gromacs VERSION 5.0.4

Diagonalizing to find eigenvectors 1 through 50...
Calculation Ritz values and Lanczos vectors, max 1000 iterations...
^MIteration1:   0 out of  50 Ritz values converged.^MIteration2:   0
out of  50 Ritz values converged.^MIteration3:   0 out of  50 Ritz values
converged.

I found a similar problem on the gmx-users but any response
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2006-February/020179.html

Do you know why my vector 1 doesn't converge ?

Best regards,

Esra KARAKAS


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[gmx-users] H-REMD in umbrella sampling

[adam]

Hi,

Is Hamiltonian REMD possible with umbrella sampling in pure gromacs 5.1 without 
plumed patch ? It should be according to gromacs 5 paper and manual but no 
details are provided of how to use it.
If yes, does anyone successfully applied it and could share sample mdp options 
used to exchange between umbrella windows ?

So far, whatever setup I use I get the message that systems are identical and 
there is nothing to exchange - seems that gromacs doesn’t recognise any 
differences in pulling options.

Thanks a lot for help!

Regards,
Adam
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Re: [gmx-users] cannot open traj.xtc

[Justin Lemkul]

On 11/20/15 2:10 AM, surbhi mahajan wrote:

Thankyou sir,
After using g_order -s md_0_1.tpr -f md_0_1.tpr.trr -n sn1.ndx -d z -od
deuter_sn1.xvg
the file order.xvg is created but still my file does not give any
information about the system whether it is in gel phase or liquid phase.


The program calculates order parameters, it doesn't do your thinking for you. 
You have to interpret the contents of the deuter_sn*.xvg files and, in 
conjunction with other qualitative and quantitative data, make an assessment of 
what your bilayer is doing.


-Justin


Please suggest me where i am going wrong.
Thanks in advance.

Regards
Surbhi
On Wed, Nov 18, 2015 at 6:11 PM, Justin Lemkul  wrote:




On 11/18/15 2:45 AM, surbhi mahajan wrote:


Dear users,
I am M.Sc student , I have been doing my simulations on lipids , I am
stuck
at the analysis part in which i want to calculate deuterium order
parameter
after I give the command:
g_order -s md_0_1.tpr -n sn1.ndx -d z -od deuter_sn1.xvg
I get the error cannot open file traj.xtc. please help me in solving this
error.



You didn't specify a trajectory file name (-f argument) so g_order looks
for the default name (traj.xtc) and it doesn't exit.  Specify a proper
input file name.

-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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--
==

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] inertia tensor

[sarman]

Dear Gromacs users,

I wonder whether it is possible to calculate the inertia tensor for the 
molecules?

Thank you in advance for the answer

Sten Sarman
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[gmx-users] Dumping centers of mass of molecules during MD simulation

[S.M. Golam Mortuza]

Dear Gromacs User,
Instead of dumping all atoms of a specific type of molecules, I would like to 
dump centers of mass (COM) of the molecules during MD simulations in Gromacs to 
reduce trajectory storage. I know g_traj can be used to dump COM of molecules 
from trajectory files. But, in that case, I've to generate the trajectory file 
first, and, that's storage consuming, since it has information of all atoms. 
Also, I know that xtc_grps in .mdp file dumps specific group of atoms/molecules 
and create traj.xtc. I am just wondering if there is any command that I can use 
in .mdp file to dump COM of the specific groups mentioned in xtc_grps. I would 
really appreciate if anyone can help me in this regard.
Thanks in advance for  your valuable time.

 Regards,Golam
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Re: [gmx-users] Gromacs 5.1 and 5.1.1 crash in REMD

[Mark Abraham]

Hi,

Yes, that's a real bug. I'm not yet sure what to do about it, but I'll
continue discussion at http://redmine.gromacs.org/issues/1848

Mark

On Thu, Nov 19, 2015 at 8:06 PM Krzysztof Kuczera  wrote:

> Dear Justin and Mark
>
> Thanks for your helpful suggestions.
> Yes, my case is just like bug 1848
> Our computing staff recompiled the 5.1.1 code with the debugger an ran
> a backtrace
> on my job, concluding that there is a bug in the code.
> I include their conclusions in case that might help resolve the problem-
> condensed backtrace follows:
> Krzysztof
>
>
> [67] 0x007a10bd in add_binr (b=0x25f11c0, nr=9, r=0x0) at
> /home/wmason/gromacs-5.1.1/src/gromacs/gmxlib/rbin.c:94
> [4-7,12-15,20-31,60-67] 94 rbuf[i] = r[i];
>
> 0x00725758 in global_stat (fplog=0x3543750, gs=0x3639420,
> cr=0x3536fa0,
> enerd=0x36398b0, fvir=0x0, svir=0x0, mu_tot=0x7fff6a2dfe6c,
> inputrec=0x35424f0,
> ekind=0x3635990, constr=0x363b920, vcm=0x0, nsig=0, sig=0x0,
> top_global=0x3541860, state_local=0x363a090, bSumEkinhOld=0, flags=146) at
> /home/wmason/gromacs-5.1.1/src/gromacs/mdlib/stat.cpp:229
>
> 0x0073efcd in compute_globals (fplog=0x3543750, gstat=0x3639420,
> cr=0x3536fa0, ir=0x35424f0, fr=0x3599df0, ekind=0x3635990, state=0x363a090,
> state_global=0x3543270, mdatoms=0x35cc860, nrnb=0x3599a20, vcm=0x3623b40,
> wcycle=0x3599340, enerd=0x36398b0, force_vir=0x0, shake_vir=0x0,
> total_vir=0x0,
> pres=0x0, mu_tot=0x7fff6a2dfe6c, constr=0x363b920, gs=0x0, bInterSimGS=0,
> box=0x363a0b0, top_global=0x3541860, bSumEkinhOld=0x7fff6a2dff10,
> flags=146) at
> /home/wmason/gromacs-5.1.1/src/gromacs/mdlib/md_support.cpp:342
>
> 0x004c3dca in do_md (fplog=0x0, cr=0x24a7fb0, nfile=35,
> fnm=0x7fffa95b48a8, oenv=0x24b46e0, bVerbose=0, bCompact=1,
> nstglobalcomm=20,
> vsite=0x252d890, constr=0x25e9a80, stepout=100, ir=0x24b2430,
> top_global=0x24b4760, fcd=0x24ea8b0, state_global=0x24b31c0,
> mdatoms=0x252d980,
> nrnb=0x24fa9b0, wcycle=0x24fa1b0, ed=0x0, fr=0x24fad80, repl_ex_nst=500,
> repl_ex_nex=0, repl_ex_seed=-1, membed=0x0, cpt_period=15, max_hours=-1,
> imdport=, Flags=1055744, walltime_accounting=0x2584a20) at
> /home/wmason/gromacs-5.1.1/src/programs/mdrun/md.cpp:969
>
> 0x004d4a64 in mdrunner (hw_opt=0x7fff6a2e1d58, fplog=0x3543750,
> cr=0x3536fa0, nfile=35, fnm=0x7fff6a2e15f8, oenv=0x35436d0, bVerbose=0,
> bCompact=1, nstglobalcomm=-1, ddxyz=0x7fff6a2e11bc, dd_node_order=1, rdd=0,
> rconstr=0, dddlb_opt=0x1f3b10c "auto", dlb_scale=0.80012, ddcsx=0x0,
> ddcsy=0x0, ddcsz=0x0, nbpu_opt=0x1f3b10c "auto", nstlist_cmdline=0,
> nsteps_cmdline=-2, nstepout=100, resetstep=-1, nmultisim=40,
> repl_ex_nst=500,
> repl_ex_nex=0, repl_ex_seed=-1, pforce=-1, cpt_period=15, max_hours=-1,
> imdport=, Flags=1055744) at
> /home/wmason/gromacs-5.1.1/src/programs/mdrun/runner.cpp:1270
>
> 0x004cb637 in gmx_mdrun (argc=15, argv=0x3531c20) at
> /home/wmason/gromacs-5.1.1/src/programs/mdrun/mdrun.cpp:537
>
> 0x0050b26b in gmx::CommandLineModuleManager::runAsMainCMain
> (argc=15,
> argv=0x7fffa95b5aa8, mainFunction=0x4c8d73 ) at
>
> /home/wmason/gromacs-5.1.1/src/gromacs/commandline/cmdlinemodulemanager.cpp:588
>
> 0x004ba316 in main (argc=15, argv=0x7fff6a2e27f8) at
> /home/wmason/gromacs-5.1.1/src/programs/mdrun_main.cpp:43
>
>
> The error is a classic segmentation fault--caused by accessing an array
> out of
> bounds. It's a bug in the Gromacs 5.1.1 code. You will need to file a bug
> report with gromacs, and they will need your job input to reproduce the
> error,
> and the backtrace info above, which I've summarized if you just want to
> read
> the code yourself:
>
> "add_rbin" in gromacs-5.1.1/src/gromacs/gmxlib/rbin.c:94
> called from "global_stat" in gromacs-5.1.1/src/gromacs/mdlib/stat.cpp:229
> called from "compute_globals" in
> gromacs-5.1.1/src/gromacs/mdlib/md_support.cpp:342
> called from "do_md" in /gromacs-5.1.1/src/programs/mdrun/md.cpp:969
> called from "mdrunner" in gromacs-5.1.1/src/programs/mdrun/runner.cpp:1270
> called from "gmx_mdrun" in gromacs-5.1.1/src/programs/mdrun/mdrun.cpp:537
>
>
> The code which fails is taking a "bin" of the "gmx_global_stat" type, which
> holds an array of doubles and the size of the array, and tries to copy in
> data
> from a "tensor" of the force virial, during a step in which energy is
> computed
> globally.
>
> I don't have any clue what this means, except for what the low-level code
> says
> (I almost always have read the source code when debugging so I could try to
> explain what's happening). There are multiple possible causes for this
> error,
> such as:
> A. The memory allocation for the "bin" fails quietly--the array is not
> resized
> (or not the right size), and then the error occurs at the next function
> which
> tries to write data there.
> B. The tensor is actually not the size "DIM*DIM" (3x3 if I'm reading
> correctly)
> that the function expects. Accessing the 

Re: [gmx-users] Dumping centers of mass of molecules during MD simulation

[Justin Lemkul]

On 11/20/15 2:53 PM, S.M. Golam Mortuza wrote:

Dear Gromacs User, Instead of dumping all atoms of a specific type of
molecules, I would like to dump centers of mass (COM) of the molecules during
MD simulations in Gromacs to reduce trajectory storage. I know g_traj can be
used to dump COM of molecules from trajectory files. But, in that case, I've
to generate the trajectory file first, and, that's storage consuming, since
it has information of all atoms. Also, I know that xtc_grps in .mdp file
dumps specific group of atoms/molecules and create traj.xtc. I am just
wondering if there is any command that I can use in .mdp file to dump COM of
the specific groups mentioned in xtc_grps. I would really appreciate if
anyone can help me in this regard.


AFAIK, there is no such feature.  This would require calculation of COM 
positions of desired group(s) every time write_traj() is called, which impairs 
performance.


-Justin

--
==

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

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

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

==
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Re: [gmx-users] Center of mass removal for a trajectory which is already created

[Faezeh Pousaneh]

To whom may have similar problem, that is how I solved it:

First of all, Gromacs by default uses center of mass removal (at least in
versions I use), but that is for 'whole system'. In my case I  have a
two-component system and I am interested in collecting density for one of
the components.
So, I used -fit obtain in trjconv to remove transnational movement of
component 2:

trjconv_mpi -fit translation -s production.tpr -f traj.xtc -o OUTPUT.xtc
chose component 2 and 2,

Then, I collect densities from produced OUTPUT.xtc.


Best regards


On Fri, Nov 13, 2015 at 1:38 PM, Faezeh Pousaneh 
wrote:

> Justin, thanks for comment.
> In fact I am going to analyze g_density, but I see center of mass moves. I
> have two-component system which has phase separated after a very long time.
> I can't redo the simulation.
> I could not mange that by tajconv.
> Can I take the final .gro file of current simulation and run it with COM
> removal to collect density?
>
>
> Best regards
>
>
> On Fri, Nov 13, 2015 at 1:30 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 11/13/15 4:06 AM, Faezeh Pousaneh wrote:
>>
>>> Hi,
>>>
>>> Please some one help me how to remove center of mass motion in a
>>> trajectory
>>> which is already created without  this setting? is that possible?
>>>
>>>
>> Not using COM motion removal during the run leads to artifacts; no amount
>> of post-processing will fix that.  If you're just looking to re-center some
>> molecule(s) of interest, that's what trjconv is for.
>>
>> -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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>> posting!
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>>
>
>
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