Re: [gmx-users] MD simulations in the presence of osmolytes

[XAvier Periole]

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

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

[SEMRAN İPEK]

Dear justin;

As usual, it is of your kindness to explain extensively. I will give it try
and let you know.

Best regards;

semran


2013/11/18 Justin Lemkul 

>
>
> On 11/15/13 6:49 AM, SEMRAN İPEK wrote:
>
>> Dear gromacs users;
>>
>> I have been trying to find out the waters close to certain residue. Here
>> is
>> my selection dat:
>>
>> waterO = name "OW";
>> close = waterO and within 0.35 of resnr 334;
>> close
>>
>>
>> **
>> I have been using the command of "g_select -f md_30.xtc -b 3 -e 3
>>   -s md_30.gro -oi index.dat -sf selection.dat"
>>
>> Somehow the code sometimes finds the waters within 0.35 nm of residue  and
>> sometimes finds the waters too far away from protein (30 nm away .)
>>
>>
> Does that distance perhaps coincide with a periodic image in which the
> distance criterion is satisfied?
>
>
>
>>
>> Could you please guide me along the process for g_select?
>>
>>
> Check to make sure all of your criteria make sense.  Write an index group
> (from g_select) that specifies just "resnr 334" to verify that the
> coordinates are being processed and that you don't need something more
> specific like 'group "Protein" and resnr 334.'
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
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[gmx-users] ERROR when generated a rtp file with "grompp"

[ookami a]

Dear all:

I have such error below:

Fatal error:
number of coordinates in coordinate file (p_wateroil.gro, 55383)
 does not match topology (topol.top, 55421)

it tells that the number of atoms are not same.
In my top file:
 [ molecules ]
; Compound#mols
Protein_chain_A 1
DOD   780
SOL  7882

I have 1*2097 + 780*38 + 7882*3 = 55383 atoms which suppose to be same in
the .gro file.

If I modified my top to
[ molecules ]
; Compound#mols
Protein_chain_A 1
DOD   779
SOL  7882

it generate such errors :
Warning: atom name 1 in topol.top and p_wateroil.gro does not match (C1 - N)
Warning: atom name 2 in topol.top and p_wateroil.gro does not match (H11 -
H1)
Warning: atom name 3 in topol.top and p_wateroil.gro does not match (H12 -
H2)
Warning: atom name 4 in topol.top and p_wateroil.gro does not match (H13 -
H3)
Warning: atom name 5 in topol.top and p_wateroil.gro does not match (C2 -
CA)
Warning: atom name 6 in topol.top and p_wateroil.gro does not match (H21 -
HA)
Warning: atom name 7 in topol.top and p_wateroil.gro does not match (H22 -
CB)
Warning: atom name 8 in topol.top and p_wateroil.gro does not match (C3 -
HB1)
Warning: atom name 9 in topol.top and p_wateroil.gro does not match (H31 -
HB2)
Warning: atom name 10 in topol.top and p_wateroil.gro does not match (H32 -
HB3)
Warning: atom name 11 in topol.top and p_wateroil.gro does not match (C4 -
C)
Warning: atom name 12 in topol.top and p_wateroil.gro does not match (H41 -
O)
Warning: atom name 13 in topol.top and p_wateroil.gro does not match (H42 -
N)
Warning: atom name 14 in topol.top and p_wateroil.gro does not match (C5 -
CD)
Warning: atom name 15 in topol.top and p_wateroil.gro does not match (H51 -
HD1)
Warning: atom name 16 in topol.top and p_wateroil.gro does not match (H52 -
HD2)
Warning: atom name 17 in topol.top and p_wateroil.gro does not match (C6 -
CG)
Warning: atom name 18 in topol.top and p_wateroil.gro does not match (H61 -
HG1)
Warning: atom name 19 in topol.top and p_wateroil.gro does not match (H62 -
HG2)
Warning: atom name 20 in topol.top and p_wateroil.gro does not match (C7 -
CB)
(more than 20 non-matching atom names)

WARNING 1 [file topol.top, line 19983]:
  2053 non-matching atom names
  atom names from topol.top will be used
  atom names from p_wateroil.gro will be ignored

Anyone knows why and how to fix it?
Thank you!
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Re: [gmx-users] nstlist and performances

[rajat desikan]

Hi,
I would be very careful about increasing nstlist for big systems. This can
lead to nonphysical phenomena, especially for highly anisotropic systems.
Check out http://pubs.acs.org/doi/abs/10.1021/ct3001359  There are other
papers too...


On Mon, Nov 18, 2013 at 9:50 PM, Mark Abraham wrote:

> On Mon, Nov 18, 2013 at 3:58 PM, Riccardo Concu 
> wrote:
>
> > Dear all,
> > I'm running a simulation of a quite big system and is running very low
> > 2ns/day. I need to boost-up the simulation speed but i don't know how. I
> > tried to use nstlist=10 but the system crash due to too many lincs
> > warning. Previously I minimized the system, then annealed and now i need
> > to run the production. All the statistics of the minimization step and
> > the anneling step seems good. Below I have attached the .mdp file.
> > Thank you,
> > Riccardo
> >
> > integrator   = md
> > tinit= 0
> > dt   = 0.002
> > nsteps   = 200;4ns
> > comm-mode= Linear
> > nstcomm  = 10
> > comm-grps= System
> > nstxout  = 25000
> > nstvout  = 25000
> > nstfout  = 25000
> > nstlog   = 25000
> > nstenergy= 25000
> > nstxtcout= 25000
> > xtc-precision= 25000
> > xtc-grps = System
> >
>
> Writing output is not free - choose to write the kinds of data you actually
> want.
>
>
> > energygrps   = NAP NA WAT MET SI3 I LI+
> >
>
> This can be costly - do this in an mdrun -rerun, on only the frames you
> want, if you actually need it.
>
>
> > nstlist  = 5
> > ns_type  = grid
> > pbc  = xyz
> > periodic_molecules   = no
> > rlist= 0.9
> > coulombtype  = PME
> > rcoulomb = 0.9
> > vdw-type = Cut-off
> > rvdw = 0.9
> > fourierspacing   = 0.12
> > fourier_nx   = 0
> > fourier_ny   = 0
> > fourier_nz   = 0
> > pme_order= 6
> >
>
> Why? Nobody does this AFAIK
>
>
> > ewald_rtol   = 1e-5
> > optimize_fft = yes
> > Tcoupl   = v-rescale
> > tc-grps  = System
> > tau_t=  0.1
> > ref_t= 298
> > Pcoupl   = Parrinello-Rahman
> > Pcoupltype   = Isotropic
> > tau_p= 1
> > compressibility  = 4.5e-5
> > ref_p= 1.01325
> > gen_vel  = yes
> >
>
> I'd follow the advice here
> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
> about
> equilibrating, which should relax the effective nstlist constraint, because
> you're not doing big volume changes with a marginally stable barostat.
>
> Then I'd do my measuring of performance over a production run, and look at
> the reports at the end of the .log file to see what's taking time that
> might be inappropriate.
>
> Mark
>
>
> > gen_temp = 298
> > gen_seed = 173529
> > constraints  = all-bonds
> > constraint-algorithm = Lincs
> > lincs-order  = 4
> > lincs-iter   = 1
> >
> >
> > --
> > gromacs.org_gmx-users mailing list
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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[gmx-users] Cannot write trajectory frame; maybe you are out of disk space?

[vsharma]

 

dear all, 
i am getting following error on giving command for NVT equilibrations:
mdrun -deffnm nvt -v -nt 8 

File input/output error: 
Cannot write trajectory frame; maybe you are out of disk space? 

i have gromacs 4.6.4 version, 12.04 ubuntu, 7.9GiB memory and 976 GB
Disk space, i am simulating 414aa long protein for 10ns. 

any help 

-- 
VANDNA
JRF
C/O Dr. Girish Sahni
Protein Science lab
Phone No. 0172-2690830
Institurte of Microbial Technology (IMTech)
Sector -39A, Chandigarh,160036
 
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Re: [gmx-users] a query

[vansh]

ok ..thanks 

-
thanks in advance :)
--
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Re: [gmx-users] installing latest version of gromacs 4.6.3

[vansh]

can you please suggest me how to get this ..i am using bash shell


-
thanks in advance :)
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[gmx-users] MD simulations in the presence of osmolytes

[Amjad Farooq]

Hi everyone,

I am wondering whether it is possible to conduct MD simulations on a
protein system in the presence of osmolytes such as TMAO and sucrose using
an explicit water model.

If not, how could this be implemented?

Does any of the force fields available in GROMACS support the inclusion of
any of these osmolytes?

Thank you for your input.




*AMJAD FAROOQ PhD DIC | Associate ProfessorDept of Biochemistry & Molecular
Biology | Miller School of Medicine | University of Miami | Miami | FL
33136Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217,
Miami , FL 33136 am...@farooqlab.net  | off
305-243-2429 | lab 305-243-9799 | fax 305-243-3955 | www.farooqlab.net
*
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[gmx-users] How to add motion of center of mass into temperature coupling?

[李亚东]

Hello All,

  I am studying amino acid diffusion in water flow.

I first tried to add y direction acceleration to all water molecules while
fix center of mass of the system. But found water molecules do not diffuse
in the y direction.

Then I tried to remove center of mass correction by setting comm-mode=None.
Then I found water molecules just keep accelerate in the y direction, which
I thought, is not quit physical.

My question is: *How to add motion of center of mass into temperature
coupling, so that the water molecules can form a steady flow in y
direction.*



Sincerely,

 Yadong
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 115, Issue 69

[Mark Abraham]

On Mon, Nov 18, 2013 at 11:11 PM, Justin Lemkul  wrote:

>
>
> On 11/18/13 5:05 PM, Hari Pandey wrote:
>
>> Dear Dr. Tsjerk,
>> Many many thanks for your help. This makes me some sense but still I am
>> confused about that you indicated me to look out the gromacs/share
>>  directory.  In my gromacs, I have following directory tree:
>> gromacs/share/gromacs/top
>> I did not found a format. I am wandering what could be that file in which
>> I can check format.
>>
>
> The atommass.dat file is in /gromacs/share/gromacs/top.
>
>
>  Other is, What I am doing my simulation is: 
> pdb2gmx--->editconf.--->genbox---grompp---mdrun.
>>  But to get (.tpr) I need to pass editconf first.
>>
>
> The output from editconf is getting confused based on the atypical
> nomenclature that you are using.  It thinks SOD is S instead of Na.  The
> .top for the system is definitive, as has been stated several times.  The
> .tpr file is built based on the .top and not the atom names.  You can
> convince yourself of the integrity of the system using gmxdump on the
> resulting .tpr file and see the correct masses.
>
>
>  Would you please let me know how do I include mass on (.pdb).
>>
>
> PDB files do not include mass.


... which is the root of the problem. Hari is choosing to name sodium SOD
in his input, and to depend on editconf being able to recognize that this
is sodium. That's a hard problem to solve in general, and editconf has only
a limited set of machinery. Rather than spend time on more powerful
machinery for a tiny use case, there's a warning that you should check
sanity. Looking ahead, most of the force fields will expect sodium atoms
and residues to be named "NA" so Hari should probably go and do that to
save further pain when grompp anxiously warns that the names don't match.
Or use the back of the nearest envelope, rather than editconf -density to
work out how many atoms go in how big a box ;-)

Mark


>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
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Re: [gmx-users] Average number of salt bridge

[bharat gupta]

Thank you Justin... that's what I was looking for ...


On Tue, Nov 19, 2013 at 2:24 AM, Justin Lemkul  wrote:

>
>
> On 11/14/13 10:18 PM, bharat gupta wrote:
>
>> Hi,
>>
>> How can I calculate the average number of salt bridges between two
>> residues
>> during the entire simulation ??...
>>
>>
> Unless you've got some wildly noncanonical residues, this is a binary
> function.  Either the salt bridge exists (1) or does not (0).  You can
> define a salt bridge a number of ways, but the easiest and most common is
> the distance between the COM of the positive and negative moieties.  Use
> g_dist over time and post-process the output to determine the fraction of
> time spent within the distance cutoff; it's a much more useful quantity.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
> --
> gromacs.org_gmx-users mailing listgromacs.org_gmx-users@
> maillist.sys.kth.se
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 115, Issue 69

[Justin Lemkul]

On 11/18/13 5:05 PM, Hari Pandey wrote:

Dear Dr. Tsjerk,
Many many thanks for your help. This makes me some sense but still I am 
confused about that you indicated me to look out the gromacs/share  directory.  
In my gromacs, I have following directory tree:
gromacs/share/gromacs/top
I did not found a format. I am wandering what could be that file in which I can 
check format.


The atommass.dat file is in /gromacs/share/gromacs/top.


Other is, What I am doing my simulation is: 
pdb2gmx--->editconf.--->genbox---grompp---mdrun.  But to get (.tpr) I need to 
pass editconf first.


The output from editconf is getting confused based on the atypical nomenclature 
that you are using.  It thinks SOD is S instead of Na.  The .top for the system 
is definitive, as has been stated several times.  The .tpr file is built based 
on the .top and not the atom names.  You can convince yourself of the integrity 
of the system using gmxdump on the resulting .tpr file and see the correct masses.



Would you please let me know how do I include mass on (.pdb).


PDB files do not include mass.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] about using do_dssp for a few residues

[Xu, Jianqing]

Sounds good!

Thank you Justin!

Kind regards,

Jianqing



-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 18 November 2013 21:51
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] about using do_dssp for a few residues



On 11/18/13 4:08 PM, jianqing wrote:
> Will appreciate if anyone could provide any suggestions!
>

The only secondary structure that should be affected would be beta-sheets, 
since their hydrogen bonding patterns are based on non-local interactions.  
Helices, bends, and turns should show up independently of any other residues.

Your initial conclusion was correct - do_dssp, like any other program, only 
considers atoms within the index file provided.

If you only care to visualize those residues of interest, manually modify the 
.xpm file.  You can make sensible figures by providing an .m2p file on the 
original .xpm so that it renders better.  The default representation is usually 
unintelligible, but proper manipulation of the x- and y-axis ratio can yield a 
very nice figure.

-Justin

--
==

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School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201

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==
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Re: [gmx-users] about using do_dssp for a few residues

[Justin Lemkul]

On 11/18/13 4:08 PM, jianqing wrote:

Will appreciate if anyone could provide any suggestions!



The only secondary structure that should be affected would be beta-sheets, since 
their hydrogen bonding patterns are based on non-local interactions.  Helices, 
bends, and turns should show up independently of any other residues.


Your initial conclusion was correct - do_dssp, like any other program, only 
considers atoms within the index file provided.


If you only care to visualize those residues of interest, manually modify the 
.xpm file.  You can make sensible figures by providing an .m2p file on the 
original .xpm so that it renders better.  The default representation is usually 
unintelligible, but proper manipulation of the x- and y-axis ratio can yield a 
very nice figure.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 115, Issue 69

[Hari Pandey]

Dear Dr. Tsjerk,
Many many thanks for your help. This makes me some sense but still I am 
confused about that you indicated me to look out the gromacs/share  directory.  
In my gromacs, I have following directory tree:
gromacs/share/gromacs/top
I did not found a format. I am wandering what could be that file in which I can 
check format.
Other is, What I am doing my simulation is: 
pdb2gmx--->editconf.--->genbox---grompp---mdrun.  But to get (.tpr) I need to 
pass editconf first.
Would you please let me know how do I include mass on (.pdb). 
Thanks alot
Hari



On Sunday, November 17, 2013 11:16 PM, Tsjerk Wassenaar  
wrote:
 
Hi Hari,

The .pdb file you use as input has no masses listed. Editconf then resorts to a 
file called atommass.dat. You can check the format in the gromacs share 
directory and put a file in the same format in the working directory. 
Alternatively, you can make a run input file (.tpr) of your system and use that 
as input to editconf. The .tpr file has the real masses, taken from the 
atomtype definitions.

Hope it helps,

Tsjerk



On Mon, Nov 18, 2013 at 4:46 AM, Hari Pandey  wrote:

Dear Gromacs users:
>I am hanging on the problems with editconf: can any one , please help me:
>my problem is editconf displays wrong value of mass of input:
>In Last post JUSTIN pointed out that he got correct value, while he run  , but 
>let me post all about my problem:
>My atomtypes.atp  has only two atoms( I make it)
>H   1.00800
>SOD 22.99
>My aminoacids.rtp has two rasidues
>[ SOD ]
>  [ atoms ]
>    SOD    SOD  1   1
>[ AIT ]
>  [ atoms ]
>    H1 H   1   0
>my aa.pdb has three atoms
>ATOM  1  H1  AIT 1  14.328 -11.667   1.544  1.00  0.00
>ATOM  2  H2  AIT 1  15.013 -11.434   0.080  1.00  0.00
>ATOM  3  SOD SOD 2   5.599   4.582   0.028  1.00  0.00
>For testing purpose I used : pdb2gmx -f aa.pdb -o aaa.pdb and I have following:
>ATOM  1  H1  AIT 1  14.328 -11.667   1.544  1.00  0.00   H
>ATOM  2  H2  AIT 1  15.013 -11.434   0.080  1.00  0.00   H
>ATOM  3  SOD SOD 2   5.599   4.582   0.028  1.00  0.00 S
>Clearly Gromacs updating my SOD atom as S atom
>When I do editconf :::  editconf -f aaa.pdb -o aa.gro -density 1; it 
>showing following output with incorrect result. I did -density because I need 
>density of input for my research:
>
>WARNING: Masses and atomic (Van der Waals) radii will be guessed
> based on residue and atom names, since they could not be
> definitively assigned from the information in your input
> files. These guessed numbers might deviate from the mass
> and radius of the atom type. Please check the output
> files if necessary.
>
>Volume  of input 1.728 (nm^3)
>Mass    of input 34.0809 (a.m.u.) ( here we can see that gromacs is taking 
>sulphur atoms mass rather that mass os SOD
>Density of input 32.7504 (g/l)
>Scaling all box vectors by 0.319943
>new system size :  0.301  0.520  0.049
>new center  :  0.373 -0.198  0.018 (nm)
>new box vectors :  0.384  0.384  0.384 (nm)
>new box angles  :  90.00  90.00  90.00 (degrees)
>new box volume  :   0.06   (nm^3)
>
>I tried every possibilities. I updated name of atoms in all files , .pdb .atp 
>and .rtp everywhere. butt no benifit. SOMEBODY HELP ME PLEASE. What might be 
>its reason. Do I have to do something in source code or may be OS plateforms 
>any any possibility. PLEASE HELP ME. THIS ERROR IS HANGING ME SINCE A MONTH.If 
>I have to do something in source code please let me know which file should be 
>that. Or if it is due to environment then please let me know how do I come 
>over this problem..
>I tried alot. I rebooted my computer, I re installed gcc 4.8.2, Cmake latest, 
>git , FFTW3, all and finally gromacs 4.6.4 very recent release but still the 
>problem not gone away.  Please help me
>
>
>
>Thanks in advance
>
>
>
>
>
>
>
>
>
>
>
> 
>
>
>
>
>
>
>On Sunday, November 17, 2013 3:01 AM, 
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>      (Bj?rn Sommer)
>   2. Re: gromacs.org_gmx-users Digest, Vol 115, Issue 68
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>
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Re: [gmx-users] about using do_dssp for a few residues

[jianqing]

Will appreciate if anyone could provide any suggestions!

Thanks a lot!!

Jianqing

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Re: [gmx-users] problems with chain IDs for huge complex

[jkrieger]

Maybe the answer is to not worry about chain identifiers until analysis
stages - you could probably just call everything chain A at the start. You
can then create an index entry for each chain. See
http://www.gromacs.org/Documentation/How-tos/Multiple_Chains

> As far as I remember in pdb format you can only use one character for
> chain
> id.
>
>
>
> On Mon, Nov 18, 2013 at 7:05 PM,  wrote:
>
>> How about naming your chains AA-AZ then BA-BZ? You probably need to
>> change
>> the chain names in the original structures rather than just renaming the
>> files.
>>
>> > Hi,
>> >
>> > I am preparing simulation of the ribosome and because of it size I am
>> > force
>> > to use A-Z and a-z to name all chains...
>> > With pdb2gmx it is not a problem but with grompp I am ending up with
>> this
>> > error (gromacs 4.6.3):
>> >
>> > Fatal error:
>> > moleculetype Protein_chain_b is redefined
>> >
>> > I figured out that for grompp Protein_chain_b and Protein_chain_B are
>> the
>> > same entry - and hence error...
>> > I changed the name of files in this fashion:
>> > Protein_chain_b -> Protein_chain_bb etc
>> > And now grompp was able to read them but it found out that there is
>> > different number of atoms between top and gro file..
>> > Any ideas or suggestions?
>> > Thanks.
>> > Best
>> >
>> > tomek
>> > --
>> > gromacs.org_gmx-users mailing list
>> > gromacs.org_gmx-users@maillist.sys.kth.se
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>> >
>>
>>
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Re: [gmx-users] to study native cluster

[Tsjerk Wassenaar]

Hey,

Maybe this is useful:
http://md.chem.rug.nl/~mdcourse/molmod2012/analysis.html

Hope it helps,

Tsjerk


On Mon, Nov 18, 2013 at 6:56 PM, Shine A  wrote:

> Sir,
>  I did an MD simulation.Now I want to combine the techniques, principal
> component (PC) analysis
> and clustering, for revealing major conformational changes in my protein
> and for finding native cluster. How can I do this in gromacs?
>
> Thanks in
> advance...
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Re: [gmx-users] problems with chain IDs for huge complex

[Tsjerk Wassenaar]

Hi Tomek,

Process each chain separately with pdb2gmx, rename the moleculetypes and
combine them again. This is scriptable, but not entirely trivial. Renaming
the moleculetype takes something like

sed '/\[ *moleculetype *\]/{p;n;s/^.*$/NEWMOLECULETYPE/p}' itpfile

Hope it helps,

Tsjerk




On Mon, Nov 18, 2013 at 8:25 PM, Tomek Wlodarski
wrote:

> As far as I remember in pdb format you can only use one character for chain
> id.
>
>
>
> On Mon, Nov 18, 2013 at 7:05 PM,  wrote:
>
> > How about naming your chains AA-AZ then BA-BZ? You probably need to
> change
> > the chain names in the original structures rather than just renaming the
> > files.
> >
> > > Hi,
> > >
> > > I am preparing simulation of the ribosome and because of it size I am
> > > force
> > > to use A-Z and a-z to name all chains...
> > > With pdb2gmx it is not a problem but with grompp I am ending up with
> this
> > > error (gromacs 4.6.3):
> > >
> > > Fatal error:
> > > moleculetype Protein_chain_b is redefined
> > >
> > > I figured out that for grompp Protein_chain_b and Protein_chain_B are
> the
> > > same entry - and hence error...
> > > I changed the name of files in this fashion:
> > > Protein_chain_b -> Protein_chain_bb etc
> > > And now grompp was able to read them but it found out that there is
> > > different number of atoms between top and gro file..
> > > Any ideas or suggestions?
> > > Thanks.
> > > Best
> > >
> > > tomek
> > > --
> > > gromacs.org_gmx-users mailing list
> > > gromacs.org_gmx-users@maillist.sys.kth.se
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Re: [gmx-users] problems with chain IDs for huge complex

[Tomek Wlodarski]

As far as I remember in pdb format you can only use one character for chain
id.



On Mon, Nov 18, 2013 at 7:05 PM,  wrote:

> How about naming your chains AA-AZ then BA-BZ? You probably need to change
> the chain names in the original structures rather than just renaming the
> files.
>
> > Hi,
> >
> > I am preparing simulation of the ribosome and because of it size I am
> > force
> > to use A-Z and a-z to name all chains...
> > With pdb2gmx it is not a problem but with grompp I am ending up with this
> > error (gromacs 4.6.3):
> >
> > Fatal error:
> > moleculetype Protein_chain_b is redefined
> >
> > I figured out that for grompp Protein_chain_b and Protein_chain_B are the
> > same entry - and hence error...
> > I changed the name of files in this fashion:
> > Protein_chain_b -> Protein_chain_bb etc
> > And now grompp was able to read them but it found out that there is
> > different number of atoms between top and gro file..
> > Any ideas or suggestions?
> > Thanks.
> > Best
> >
> > tomek
> > --
> > gromacs.org_gmx-users mailing list
> > gromacs.org_gmx-users@maillist.sys.kth.se
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
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Re: [gmx-users] problems with chain IDs for huge complex

[jkrieger]

How about naming your chains AA-AZ then BA-BZ? You probably need to change
the chain names in the original structures rather than just renaming the
files.

> Hi,
>
> I am preparing simulation of the ribosome and because of it size I am
> force
> to use A-Z and a-z to name all chains...
> With pdb2gmx it is not a problem but with grompp I am ending up with this
> error (gromacs 4.6.3):
>
> Fatal error:
> moleculetype Protein_chain_b is redefined
>
> I figured out that for grompp Protein_chain_b and Protein_chain_B are the
> same entry - and hence error...
> I changed the name of files in this fashion:
> Protein_chain_b -> Protein_chain_bb etc
> And now grompp was able to read them but it found out that there is
> different number of atoms between top and gro file..
> Any ideas or suggestions?
> Thanks.
> Best
>
> tomek
> --
> gromacs.org_gmx-users mailing list
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Re: [gmx-users] a query

[jkrieger]

Try sending your problem in the same way you sent this email. They should
be the same.

Maybe it hadn't processed your subscription at the time you sent your
problem and now it will work.

>
>
> i have posted a problem in gronacs user forum ...but its saying that it
> is not accepted by the mailing list yet..
>
> althuogh i am already a subscriber to it..
>
> please suggest
>
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> JRF
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[gmx-users] problems with chain IDs for huge complex

[Tomek Wlodarski]

Hi,

I am preparing simulation of the ribosome and because of it size I am force
to use A-Z and a-z to name all chains...
With pdb2gmx it is not a problem but with grompp I am ending up with this
error (gromacs 4.6.3):

Fatal error:
moleculetype Protein_chain_b is redefined

I figured out that for grompp Protein_chain_b and Protein_chain_B are the
same entry - and hence error...
I changed the name of files in this fashion:
Protein_chain_b -> Protein_chain_bb etc
And now grompp was able to read them but it found out that there is
different number of atoms between top and gro file..
Any ideas or suggestions?
Thanks.
Best

tomek
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[gmx-users] to study native cluster

[Shine A]

Sir,
 I did an MD simulation.Now I want to combine the techniques, principal
component (PC) analysis
and clustering, for revealing major conformational changes in my protein
and for finding native cluster. How can I do this in gromacs?

Thanks in
advance...
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Re: [gmx-users] Membrane is shifted a lot during umbrella sampling

[sudipta]

Hi Chris,

The lipid of my system is DPPC, which is a neutral. However, the peptide is
positively charged polyarginine. The membrane is shifted a lot when the
peptide is embedded within it (i,e peptide restrained at the bilayer
region). Therefore presence of peptide inside the membrane produces such
migration in presence of electric field. Although, it is physically
meaningful, but do you think calculation of potential of mean force of such
system in presence of electric field is meaningful. I am not quite sure
about this.

Sudipta



On Fri, Oct 4, 2013 at 10:32 AM, Christopher Neale <
chris.ne...@mail.utoronto.ca> wrote:

> Dear Sudipta:
>
> on average, bilayers migrate along the positive z axis during gromacs
> simulations with a variety of atomistic force fields. This has been
> reported before, but never fully resolved (
> http://redmine.gromacs.org/issues/165 suggests it is due to rounding )
> and I see it all the time. It is not that rapid, but in microsecond-scale
> simulations it is quite obvious and statistically significant (i.e., we're
> not talking about something I've seen in one simulation ... the chance that
> this "upward" drift is due to random noise that could lead to drift along
> plus or minus z are vanishingly small). I presume that an electric field
> could magnify this incorrect behaviour. That said, if your membrane has a
> net charge, or contains an embedded protein with a net charge, then I
> expect that migration along the applied field is actually the proper
> behaviour.
>
> There are a few ways that you could stop drift along the z axis. One is to
> use the pull code to restrain your bilayer COM to (0,0,0) or some other
> absolute position (i.e., no reference group selected in the pull code) and
> only turn on the Z component of the pull force. You could also set
> comm-grps to remove COM motion of the bilayer only (hopefully somebody else
> will let me know if that is a bad idea for some reason).
>
> Chris.
>
> -- original message --
>
> I am facing problem for doing umbrella sampling simulation for the
> transferring of a small peptide across a membrene in presence of electric
> field. Moreover, the simulation was carried out at constant area. Martini
> force field for protein, lipid and water was used for this simulation. The
> electric field was applied along the -z direction across the membrane. The
> problem, which I am facing is that the position of membrane is shifted a
> lot during this this simulation. Moreover, I notice the shifting of
> membrane is significantly enhanced when I apply high electric filed. I
> don't have any clue for this shifting problem. If anyone have  idea to
> arrest the shifting problem then please share it. A copy of my input file
> is attached herewith.
>
> Thanks in advance
> Sudipta
>
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Re: [gmx-users] installing latest version of gromacs 4.6.3

[Justin Lemkul]

On 11/18/13 11:54 AM, vansh wrote:

do i need to source it every time i will use gromacs ??
as this is what happening in my case..



If you don't configure your shell startup scripts to do it for you, yes. 
Otherwise, the 'source' statement can be added to whatever startup script your 
shell uses.


-Justin

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Re: [gmx-users] RF0 and g_energy

[Justin Lemkul]

On 11/18/13 10:40 AM, Williams Ernesto Miranda Delgado wrote:

Hello
I made a rerun on a MD simulation using Reaction-Field-zero for
electrostatics. When I analyze the *.edr file with g_energy, there appears
Coul-SR and Coul-14. How can I get the Coulomb long range term? This is
very important for making LIE calculations.


I answered this already:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-November/085445.html

-Justin

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Re: [gmx-users] setting up simulation with mixed chain (nucleotide + amino acid)

[Justin Lemkul]

On 11/18/13 8:26 AM, Tomek Wlodarski wrote:

Hi,

I would like to run simulation of short peptide (nascent chain) bound to
tRNA (in amber ff).
Do gromacs supports chains which have both protein and nucleic acid
components?
I have problem with termini of this chain:
gromacs is trying to find 3'- terminus of RNA - but it can't because
terminus of the chain is amino acid type...
I know that I have to parametrize bond between nucleotide and protein.
Should I change type of this chain to either RNA or protein - e.g. by
creating special class in aminoacid.rtp which includes nucleotides (with
new names)?


You'll probably have to write the protein and RNA as separate chains in the 
input coordinate file, then use specbond.dat to assign the bond in conjunction 
with pdb2gmx -chainsep and/or -merge.


-Justin

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Re: [gmx-users] energy minimization erorr

[Justin Lemkul]

On 11/18/13 2:36 AM, Archana Sonawani-Jagtap wrote:

Hi,

I am simulating a peptide in TFE-water system. I am getting following error:
1 particles communicated to PME node 4 are more than 2/3 times the
cut-off out o f the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated.

below is my em.mdp file

integrator  = steep
emtol   = 1000.0
emstep  = 0.01
nsteps  = 5
nstlist = 1
ns_type = grid
rlist   = 1.2
coulombtype = PME
rcoloumb= 1.2
rvdw= 1.2
pbc = xyz

Please help me. Why this error has ocurred and what parameter should I
change to resolve it.


Likely the cutoffs are simply wrong, but you haven't said what the force field 
is.  The other possible sources of problems during EM are (1) bad topology or 
(2) unreasonable starting configuration.


-Justin

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==

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Health Sciences Facility II, Room 601
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Baltimore, MD 21201

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Re: [gmx-users] help about logfile

[Justin Lemkul]

On 11/17/13 9:06 PM, cqgzc wrote:

Hi Justin:
Thanks for your reply.
I checked the initial setting and the output file about simulation control
(mdout.mdp and .log file) and found that it's ok. There are some strange
results related to sample frequency (Statistics over *** steps using ***
frames in .log file) as described below:
  Statistics over 101 steps using 40001 frames
where,
nsteps=10,dt=0.001,nstlog=40,nstvout=40,nstxtcout=40,nstcalcenergy=50,nstenergy
=100
nstlist=10
 Statistics over 6001 steps using 481 frames
where,
nsteps=6000,dt=0.001,nstlog=15,nstvout=15,nstxtcout=15,nstcalcenergy=50,nstenergy=100
nstlist=10
Specially, when
nsteps=6000,dt=0.001,nstlog=50,nstvout=50,nstxtcout=50,nstcalcenergy=100,nstenergy=100
nstlist=10
It presented the following information:
Statistics over 6001 steps using 121 frames
Therefore, I really want to know how to control the sample frequency.



That's what nstlog is doing.

-Justin

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==

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School of Pharmacy
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University of Maryland, Baltimore
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Re: [gmx-users] how to pull both side

[Justin Lemkul]

On 11/17/13 8:48 AM, Tom wrote:

Dear All,

Can gromacs pull both sides (end) of a body way?
for example pulling two end of a cylinder unitl it breaks.

I knew Gromacs can pull two bodies (A and B) objects away.

Can someone inform about this functionality of pulling (both
sides/end of a same body)?



You can specify multiple pull groups (pull_group[12]) and no reference group 
(pull_group0), but I have no idea if that will work.  Otherwise, you could 
specify pull_group0 as the COM of the cylinder, and pull_group[12] as the ends.


-Justin

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==

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School of Pharmacy
Health Sciences Facility II, Room 601
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20 Penn St.
Baltimore, MD 21201

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Re: [gmx-users] membrane protein tutorial

[Justin Lemkul]

On 11/15/13 10:04 AM, leila karami wrote:

Dear Justin

I am using your tutorial (membrane protein) for my system.

I inserted my peptid into lipid bilayer. Now I want to solvate with
water using genbox tool.
To remove those water molecules are into lipid bilayer, I want to use
keepbyz.pl script by Chris Neale. In step 4 of this script:

4. use vi to edit keepbyz.pl
- upperz and lowerz variables as you please
- sol to the name of your solvent molecule

How to select upperz and lowerz? Based on what criterion?


These values specify the upper and lower bounds of the hydrophobic region of the 
membrane, i.e. the space between which you do not want any water.



If I want to have z vector = 9 nm after solvation, which value of
upperz and lowerz are appropriate?



Define the box and everything within it with editconf and decide from there.


If I use another way, only reduction of the value of C from
0.15 to 0.375 in vdwradii.dat file is enough?



It is "enough" in most general cases, but it's not foolproof.

-Justin

--
==

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School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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Re: [gmx-users] g_select

[Justin Lemkul]

On 11/15/13 6:49 AM, SEMRAN İPEK wrote:

Dear gromacs users;

I have been trying to find out the waters close to certain residue. Here is
my selection dat:

waterO = name "OW";
close = waterO and within 0.35 of resnr 334;
close


**
I have been using the command of "g_select -f md_30.xtc -b 3 -e 3
  -s md_30.gro -oi index.dat -sf selection.dat"

Somehow the code sometimes finds the waters within 0.35 nm of residue  and
sometimes finds the waters too far away from protein (30 nm away .)



Does that distance perhaps coincide with a periodic image in which the distance 
criterion is satisfied?





Could you please guide me along the process for g_select?



Check to make sure all of your criteria make sense.  Write an index group (from 
g_select) that specifies just "resnr 334" to verify that the coordinates are 
being processed and that you don't need something more specific like 'group 
"Protein" and resnr 334.'


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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Re: [gmx-users] Average number of salt bridge

[Justin Lemkul]

On 11/14/13 10:18 PM, bharat gupta wrote:

Hi,

How can I calculate the average number of salt bridges between two residues
during the entire simulation ??...



Unless you've got some wildly noncanonical residues, this is a binary function. 
 Either the salt bridge exists (1) or does not (0).  You can define a salt 
bridge a number of ways, but the easiest and most common is the distance between 
the COM of the positive and negative moieties.  Use g_dist over time and 
post-process the output to determine the fraction of time spent within the 
distance cutoff; it's a much more useful quantity.


-Justin

--
==

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Re: [gmx-users] installing latest version of gromacs 4.6.3

[vansh]

do i need to source it every time i will use gromacs ??
as this is what happening in my case..


-
thanks in advance :)
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Re: [gmx-users] nstlist and performances

[Mark Abraham]

On Mon, Nov 18, 2013 at 3:58 PM, Riccardo Concu  wrote:

> Dear all,
> I'm running a simulation of a quite big system and is running very low
> 2ns/day. I need to boost-up the simulation speed but i don't know how. I
> tried to use nstlist=10 but the system crash due to too many lincs
> warning. Previously I minimized the system, then annealed and now i need
> to run the production. All the statistics of the minimization step and
> the anneling step seems good. Below I have attached the .mdp file.
> Thank you,
> Riccardo
>
> integrator   = md
> tinit= 0
> dt   = 0.002
> nsteps   = 200;4ns
> comm-mode= Linear
> nstcomm  = 10
> comm-grps= System
> nstxout  = 25000
> nstvout  = 25000
> nstfout  = 25000
> nstlog   = 25000
> nstenergy= 25000
> nstxtcout= 25000
> xtc-precision= 25000
> xtc-grps = System
>

Writing output is not free - choose to write the kinds of data you actually
want.


> energygrps   = NAP NA WAT MET SI3 I LI+
>

This can be costly - do this in an mdrun -rerun, on only the frames you
want, if you actually need it.


> nstlist  = 5
> ns_type  = grid
> pbc  = xyz
> periodic_molecules   = no
> rlist= 0.9
> coulombtype  = PME
> rcoulomb = 0.9
> vdw-type = Cut-off
> rvdw = 0.9
> fourierspacing   = 0.12
> fourier_nx   = 0
> fourier_ny   = 0
> fourier_nz   = 0
> pme_order= 6
>

Why? Nobody does this AFAIK


> ewald_rtol   = 1e-5
> optimize_fft = yes
> Tcoupl   = v-rescale
> tc-grps  = System
> tau_t=  0.1
> ref_t= 298
> Pcoupl   = Parrinello-Rahman
> Pcoupltype   = Isotropic
> tau_p= 1
> compressibility  = 4.5e-5
> ref_p= 1.01325
> gen_vel  = yes
>

I'd follow the advice here
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
about
equilibrating, which should relax the effective nstlist constraint, because
you're not doing big volume changes with a marginally stable barostat.

Then I'd do my measuring of performance over a production run, and look at
the reports at the end of the .log file to see what's taking time that
might be inappropriate.

Mark


> gen_temp = 298
> gen_seed = 173529
> constraints  = all-bonds
> constraint-algorithm = Lincs
> lincs-order  = 4
> lincs-iter   = 1
>
>
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Re: [gmx-users] Membrane is shifted a lot during umbrella sampling

[sudipta]

Hi All,

Thank you very much for your kind reply. But obviously, if I put some
position restraints on membrane then there will be some artifacts.

Also, Chris has mentioned that it is a kind of bug in gromacs. please help
me how do I resolve this issue


sudipta


On Fri, Oct 4, 2013 at 9:33 PM, Justin Lemkul  wrote:

>
>
> On 10/4/13 10:32 AM, Christopher Neale wrote:
>
>> Dear Sudipta:
>>
>> on average, bilayers migrate along the positive z axis during gromacs
>> simulations with a variety of atomistic force fields. This has been
>> reported
>> before, but never fully resolved ( http://redmine.gromacs.org/issues/165
>> suggests it is due to rounding ) and I see it all the time. It is not that
>> rapid, but in microsecond-scale simulations it is quite obvious and
>> statistically significant (i.e., we're not talking about something I've
>> seen
>> in one simulation ... the chance that this "upward" drift is due to random
>> noise that could lead to drift along plus or minus z are vanishingly
>> small).
>>
>
> FWIW, I recall the same effect being reported for CG force fields not too
> long ago.
>
>
>  I presume that an electric field could magnify this incorrect behaviour.
>> That
>> said, if your membrane has a net charge, or contains an embedded protein
>> with
>> a net charge, then I expect that migration along the applied field is
>> actually the proper behaviour.
>>
>> There are a few ways that you could stop drift along the z axis. One is to
>> use the pull code to restrain your bilayer COM to (0,0,0) or some other
>> absolute position (i.e., no reference group selected in the pull code) and
>> only turn on the Z component of the pull force. You could also set
>> comm-grps
>> to remove COM motion of the bilayer only (hopefully somebody else will
>> let me
>> know if that is a bad idea for some reason).
>>
>>
> That sounds suspicious to me.  I think you'd end up with artifacts, not
> the least of which would be the bilayer potentially crashing into water
> molecules.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
>
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Re: [gmx-users] RF0 and g_energy

[Williams Ernesto Miranda Delgado]

Hello
I made a rerun on a MD simulation using Reaction-Field-zero for
electrostatics. When I analyze the *.edr file with g_energy, there appears
Coul-SR and Coul-14. How can I get the Coulomb long range term? This is
very important for making LIE calculations.
I used AMBER99SB FF and
rlist = 1.2
rcoul = 0.9
coultype = Reaction-Field-zero
vdw = cut-off
rvdw = 1.4
Are these parameters ok?
Thank you




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Re: [gmx-users] (no subject)

[Mark Abraham]

On Mon, Nov 18, 2013 at 2:28 PM, Shima Arasteh
wrote:

> Dear gmx users,
>
>
> My simulated system contains is composed of lipid, protein and water
> molecules.
> The NPT and NVT steps were done with position restraints on protein atoms.
> Then I removed the position restraints by line ";define  = -DPOSRES_LIPID
> -DPOSRES". But I still see the position restraint term in md.log file,
> however it seems to be small.
>
> Forexample as below:
>
>
>Energies (kJ/mol)
>BondU-BProper Dih.  Improper Dih.  CMAP Dih.
> 4.22077e+032.41766e+041.67865e+041.72538e+02   -1.02944e+01
>   LJ-14 Coulomb-14LJ (SR)  Disper. corr.   Coulomb (SR)
> 2.65248e+03   -3.79682e+041.09363e+04   -1.49330e+03   -2.05391e+05
>Coul. recip. Position Rest.  PotentialKinetic En.   Total Energy
>-9.97720e+024.84025e+01   -1.86867e+056.61349e+04   -1.20732e+05
> Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
> 3.12903e+02   -1.07476e+022.87101e+021.52447e-06
>
> Would you please let me know what this term means? And why position
> restraints still exist? Is this amount of position restraint affects the
> results significantly?
>

Use grompp -pp to see the results of how grompp interpreted all of your
inputs. There will be a position_restraints directive there somewhere, from
which you can work backwards to see its origin.

Mark



>
> Thanks in advance. I appreciate your suggestions.
>
>
>
> Sincerely,
> Shima
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Re: [gmx-users] Windows/x64, VCVS2012 compiled, crash on checkpoint writing

[Mark Abraham]

On Fri, Nov 15, 2013 at 6:43 PM, Mirco Wahab <
mirco.wa...@chemie.tu-freiberg.de> wrote:

> Gromacs 4.6.4 compiles (and links) perfectly w/VS2012
> and nvcc from CUDA 5.5 on windows/x64
> (MSVC 2012 Version 11.0.60610.01 Update 3).
>
> But -- when compiled with VS2012 (because of linking
> against CUDA 5.5 is only possible then - in contrast
> to VS2010), mdrun crashes on writing the checkpoint file.
>
> This will not happen when compiling with VS2010
> (but this exludes using of CUDA 5.5, only 5.0 is
> supported).
>
> I did set up a debugging session in VS2012 in order
> to determine the exception location (see below, on
> entry into the named function). mdrun has been compiled
> as "Release w/DebugInfo".
>
> (This has been possibly also been a problem in 4.6.3, iirc.)
>

Almost certainly a problem for the whole 4.6 series, if my theory below is
correct.


>
>
> - d:\libsrc\gromacs\gromacs-4.6.4\src\gmxlib\gmxfio.c 
>
>
> /* internal variant of get_file_md5 that operates on a locked file */
> static int gmx_fio_int_get_file_md5(t_fileio *fio, gmx_off_t offset,
> unsigned char digest[])
> {
> 7FF7B25B74C0  mov qword ptr [state],rbx
> 7FF7B25B74C5  pushrbp
> 7FF7B25B74C6  pushrsi
> 7FF7B25B74C7  pushrdi
> 7FF7B25B74C8  mov eax,100090h
> 
> 7FF7B25B74CD  call__chkstk (07FF7B28B4160h)  <== exception
>

This is supposed to automagically deal with the large allocation on the
stack (http://support.microsoft.com/kb/100775,
http://stackoverflow.com/questions/8400118/what-is-the-purpose-of-the-chkstk-function).
It seems there are compiler options that might disable/cripple the __chkstk
call, so if CUDA or GROMACS is being evil there, we'd want to have a look
at / change the command-line flags that were used in practice. Can you look
those up for us, please Mirco?


> 
> 7FF7B25B74D2  sub rsp,rax
> 7FF7B25B74D5  mov rax,qword ptr [__security_cookie
> (07FF7B29963E0h)]
> 7FF7B25B74DC  xor rax,rsp
> 7FF7B25B74DF  mov qword ptr [rsp+100080h],rax
> 7FF7B25B74E7  mov rsi,rdx
> /*1MB: large size important to catch almost identical files */
> #define CPT_CHK_LEN  1048576
> md5_state_t   state;
> unsigned char buf[CPT_CHK_LEN];
>

I can see no reason why this should be done on the stack, but neither can I
see a good reason why it should fail.

Supporting machinery for being able to have an automated test
"CanWriteCheckpoint" is on the table for 5.0, which might have prevented
this from occuring.

Mark


> gmx_off_t read_len;
> gmx_off_t seek_offset;
> int   ret = -1;
>
> seek_offset = offset - CPT_CHK_LEN;
> if (seek_offset < 0)
> 7FF7B25B74EA  xor eax,eax
> 7FF7B25B74EC  add rdx,0FFF0h
> 7FF7B25B74F3  cmovs   rdx,rax
> 7FF7B25B74F7  mov rdi,rcx
> {
> --
>
> --
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[gmx-users] nstlist and performances

[Riccardo Concu]

Dear all,
I'm running a simulation of a quite big system and is running very low
2ns/day. I need to boost-up the simulation speed but i don't know how. I
tried to use nstlist=10 but the system crash due to too many lincs
warning. Previously I minimized the system, then annealed and now i need
to run the production. All the statistics of the minimization step and
the anneling step seems good. Below I have attached the .mdp file.
Thank you,
Riccardo 

integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 200;4ns
comm-mode= Linear
nstcomm  = 10
comm-grps= System
nstxout  = 25000
nstvout  = 25000
nstfout  = 25000
nstlog   = 25000
nstenergy= 25000
nstxtcout= 25000
xtc-precision= 25000
xtc-grps = System
energygrps   = NAP NA WAT MET SI3 I LI+
nstlist  = 5
ns_type  = grid
pbc  = xyz
periodic_molecules   = no
rlist= 0.9
coulombtype  = PME
rcoulomb = 0.9
vdw-type = Cut-off
rvdw = 0.9
fourierspacing   = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order= 6
ewald_rtol   = 1e-5
optimize_fft = yes
Tcoupl   = v-rescale
tc-grps  = System
tau_t=  0.1
ref_t= 298
Pcoupl   = Parrinello-Rahman
Pcoupltype   = Isotropic
tau_p= 1
compressibility  = 4.5e-5
ref_p= 1.01325
gen_vel  = yes
gen_temp = 298
gen_seed = 173529
constraints  = all-bonds
constraint-algorithm = Lincs
lincs-order  = 4
lincs-iter   = 1


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Re: [gmx-users] GROMACS-4.6.3 CUDA version on multiple nodes each having 2 GPUs

[Mark Abraham]

On Mon, Nov 18, 2013 at 12:06 PM, Prajapati, Jigneshkumar Dahyabhai <
j.prajap...@jacobs-university.de> wrote:

> Hi Carsten,
>
> Thanks for reply. Everything is working fine on single node. The problem
> starts when I move to two nodes.
>
> I have tried with the option that you have mentioned earlier and this is
> the error I got ,
> mpirun -np 4 mdrun
>
> mismatching number of PP MPI processes and GPUs per node.
> mdrun was started with 4 PP MPI processes per node, but only 2 GPUs were
> detected.
>

That sounds like your hostfile / mpirun command line is not set up so that
mpirun knows to dispatch two processes to each node.

Mark


>
> Likewise, I have tried many options and on many occasions job runs but
> without using GPUs on second node . More specifically, my problem is when I
> use two nodes each having two GPU cards, GROMACS detects GPUs on first node
> only. It fails to detect GPU cards on second node (check the em.log file in
> attachments). I am not sure what is the reason. Please let me know if I
> could try something else.
>
> Thank you.
>
> -Jignesh
>
>
>
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Carsten
> Kutzner [ckut...@gwdg.de]
> Sent: Thursday, November 14, 2013 10:54 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] GROMACS-4.6.3 CUDA version on multiple nodes each
>  having 2 GPUs
>
> Hi,
>
> if you run on a single node with 2 GPUs, this command line should work:
>
> > mpirun -np 2  mdrun -v -deffnm $configfile
>
> If you run on two nodes, try this:
> mpirun -np 4 mdrun
>
> Choosing -np equal to the total number of GPUs should work (although it
> might
> not be the best option performance-wise).
>
> For a better performance you can try
> mpirun -np 4 mdrun -gpu_id 0011on a single node
> or
> mpirun -np 8 mdrun -gpu_id 0011on two nodes
>
> Carsten
>
>
> On Nov 13, 2013, at 7:55 PM, "Prajapati, Jigneshkumar Dahyabhai" <
> j.prajap...@jacobs-university.de> wrote:
>
> > Hello,
> >
> > I am trying to run MPI, OpenMP and CUDA enable GROMACS 4.6.3 on nodes
> having 12 cores (2 CPUs) and 2 GPUs (Tesla M2090) each. The problem is when
> I launch job GROMCAS is using only GPUs on first node come across and
> failing to use GPUs on other nodes.
> >
> > The command I used for two gpu enable nodes was,
> >
> > mpirun -np 2  mdrun -v -deffnm $configfile
> >
> > I tried with many other options but none of them worked. The one thing
> needs to remember here is that on all the nodes, GPUs got id 0 and 1 so
> -gpu_id option also didn't work.
> >
> > This old thread gave me some idea but I didn't understand it completely.
> > http://lists.gromacs.org/pipermail/gmx-users/2013-March/079802.html
> >
> > Please suggests me the possible solutions for this issue.
> >
> > Thank you
> > --Jignesh
> > --
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>
>
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/grubmueller/kutzner
> http://www.mpibpc.mpg.de/grubmueller/sppexa
>
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[gmx-users] position restraint term

[Shima Arasteh]

Dear gmx users,


My simulated system contains is composed of lipid, protein and water molecules.
The NPT and NVT steps were done with position restraints on protein atoms. Then 
I removed the position restraints by line ";define  = -DPOSRES_LIPID -DPOSRES". 
But I still see the position restraint term in md.log file, however it seems to 
be small.

Forexample as below:


   Energies (kJ/mol)
   Bond    U-B    Proper Dih.  Improper Dih.  CMAP Dih.
    4.22077e+03    2.41766e+04    1.67865e+04    1.72538e+02   -1.02944e+01
  LJ-14 Coulomb-14    LJ (SR)  Disper. corr.   Coulomb (SR)
    2.65248e+03   -3.79682e+04    1.09363e+04   -1.49330e+03   -2.05391e+05
   Coul. recip. Position Rest.  Potential    Kinetic En.   Total Energy
   -9.97720e+02    4.84025e+01   -1.86867e+05    6.61349e+04   -1.20732e+05
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.12903e+02   -1.07476e+02    2.87101e+02    1.52447e-06

Would you please let me know what this term means? And why position restraints 
still exist? Is this amount of position restraint affects the results 
significantly? 


Thanks in advance. I appreciate your suggestions.



Sincerely,
Shima 
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[gmx-users] position restraint term

[Shima Arasteh]

Dear gmx users,


My simulated system contains is composed of lipid, protein and water molecules.
The NPT and NVT steps were done with position restraints on protein atoms. Then 
I removed the position restraints by line ";define  = -DPOSRES_LIPID -DPOSRES". 
But I still see the position restraint term in md.log file, however it seems to 
be small.

Forexample as below:


   Energies (kJ/mol)
   Bond    U-B    Proper Dih.  Improper Dih.  CMAP Dih.
    4.22077e+03    2.41766e+04    1.67865e+04    1.72538e+02   -1.02944e+01
  LJ-14 Coulomb-14    LJ (SR)  Disper. corr.   Coulomb (SR)
    2.65248e+03   -3.79682e+04    1.09363e+04   -1.49330e+03   -2.05391e+05
   Coul. recip. Position Rest.  Potential    Kinetic En.   Total Energy
   -9.97720e+02    4.84025e+01   -1.86867e+05    6.61349e+04   -1.20732e+05
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.12903e+02   -1.07476e+02    2.87101e+02    1.52447e-06

Would you please let me know what this term means? And why position restraints 
still exist? Is this amount of position restraint affects the results 
significantly? 


Thanks in advance. I appreciate your suggestions.



Sincerely,
Shima 
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[gmx-users] (no subject)

[Shima Arasteh]

Dear gmx users,


My simulated system contains is composed of lipid, protein and water molecules.
The NPT and NVT steps were done with position restraints on protein atoms. Then 
I removed the position restraints by line ";define  = -DPOSRES_LIPID -DPOSRES". 
But I still see the position restraint term in md.log file, however it seems to 
be small.

Forexample as below:


   Energies (kJ/mol)
   Bond    U-B    Proper Dih.  Improper Dih.  CMAP Dih.
    4.22077e+03    2.41766e+04    1.67865e+04    1.72538e+02   -1.02944e+01
  LJ-14 Coulomb-14    LJ (SR)  Disper. corr.   Coulomb (SR)
    2.65248e+03   -3.79682e+04    1.09363e+04   -1.49330e+03   -2.05391e+05
   Coul. recip. Position Rest.  Potential    Kinetic En.   Total Energy
   -9.97720e+02    4.84025e+01   -1.86867e+05    6.61349e+04   -1.20732e+05
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.12903e+02   -1.07476e+02    2.87101e+02    1.52447e-06

Would you please let me know what this term means? And why position restraints 
still exist? Is this amount of position restraint affects the results 
significantly? 


Thanks in advance. I appreciate your suggestions.



Sincerely,
Shima 
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[gmx-users] setting up simulation with mixed chain (nucleotide + amino acid)

[Tomek Wlodarski]

Hi,

I would like to run simulation of short peptide (nascent chain) bound to
tRNA (in amber ff).
Do gromacs supports chains which have both protein and nucleic acid
components?
I have problem with termini of this chain:
gromacs is trying to find 3'- terminus of RNA - but it can't because
terminus of the chain is amino acid type...
I know that I have to parametrize bond between nucleotide and protein.
Should I change type of this chain to either RNA or protein - e.g. by
creating special class in aminoacid.rtp which includes nucleotides (with
new names)?
I would be very grateful for any suggestions.
Thank you.
Best,

tomek
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Re: [gmx-users] can not write coordinate file when running ibi

[Chandan Choudhury]

Dear Zhichen,

This is not the appropriate forum for your query. It seems you are using
votca for coarse grained simulations. Please post at
votca@googlegroups.comrelating all your votca queries.

Chandan


--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Mon, Nov 18, 2013 at 10:49 AM, cqgzc  wrote:

> Hi:
> When I am running the ibi procedure, I get the following error message:
> A coordinate in file conf.gro does not contain a '.'
> Additionally, I check the coordinate file of confout.gro in step_001. It
> showed that 'nan' symbol appeared in confout.gro. Just like:
> 856
> 1RDXRDX1 nan nan-nan nan nan-nan
> 2RDXRDX2 nan nan-nan nan nan-nan
> 3RDXRDX3 nan nan-nan nan nan-nan
> 4RDXRDX4 nan nan-nan nan nan-nan
> 5RDXRDX5 nan nan-nan nan nan-nan
> 6RDXRDX6 nan nan-nan nan nan-nan
> 7RDXRDX7 nan nan-nan nan nan-nan
> What is wrong with this? How can I fix it? I am very appreciating for
> anyone's help.
> Best Wishes!
> Zhicheng Guo
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/can-not-write-coordinate-file-when-running-ibi-tp5012535.html
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Re: [gmx-users] Cannot write trajectory frame; maybe you are out of disk space?

[Mark Abraham]

Run somewhere where you have write permissions, like your home directory.
Don't run in root file space, or as root!

Mark
On Nov 18, 2013 1:04 PM, "vansh"  wrote:

> dear all,
> i am getting following error on giving command:  mdrun -deffnm nvt -v -nt 8
> File input/output error:
> Cannot write trajectory frame; maybe you are out of disk space?
>
> i have gromacs 4.6.4 version, 12.04 ubuntu, 7.9GiB memory and 976 GB Disk
> space, i am simulating 414aa long protein for 10ns.
>
> any help
>
> -
> thanks in advance :)
> --
> View this message in context:
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Re: [gmx-users] Replicating triclinic unit cells

[Mark Abraham]

genconf can't replicate the triclinic cell that you gave it (e.g. created
with editconf)?

Mark


On Sun, Nov 17, 2013 at 9:04 PM, Eudes Fileti  wrote:

> Hi GMX users
> I need replicate a triclinic unit cell. However, both
> genconf and topotools (VMD plugin) generate only
> orthorrombic cells. Anyone knows some free software
> or script to do that?
> eef
> ___
> Eudes Eterno Fileti
> Instituto de Ciência e Tecnologia da UNIFESP
> Rua Talim, 330, São José dos Campos - SP
> Página: sites.google.com/site/fileti/
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Re: [gmx-users] installing latest version of gromacs 4.6.3

[Mark Abraham]

Your system is configured such that it recognizes the (old) version of
GROMACS you could get with the command it lists. Since you want the latest
version (which is no longer 4.6.3!) do what you've done and make sure you
finish reading
http://www.gromacs.org/Documentation/Installation_Instructions#4.11._Getting_access_to_GROMACS_after_installation

Mark


On Sun, Nov 17, 2013 at 10:30 AM, vansh  wrote:

>
> hello all,
>
> I followed below mentioned instructions on how to install latest version of
> GROMACS latest version of Gromacs and installed it but now when I run
> gromacs, it is telling me gromacs is not install you can install it by
> typing "sudo apt-get install gromacs" which is just installing it from
> repository? any comments? I want to install gromacs 4.6.3 and be able to
> run
> it from anywhere in terminal.
>
> tar xfz gromacs-4.6.3.tar.gz
> cd gromacs-4.6.3
> mkdir build
> cd build
> cmake .. -DGMX_BUILD_OWN_FFTW=ON
> make
> sudo make install
>
> please help..:)
>
> -
> thanks in advance :)
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/installing-latest-version-of-gromacs-4-6-3-tp5012529.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] GROMACS-4.6.3 CUDA version on multiple nodes each having 2 GPUs

[Prajapati, Jigneshkumar Dahyabhai]

Hi Szilárd,

My apologies for misunderstanding. The old thread I mentioned is not mine, I 
just found it on website. 

Unlike that thread, our nodes have homogeneous hardware. I tried all the 
options and everything looks perfect on a single node. I started to  face 
problems  when I switched to two nodes. I could run the job on many occasions 
but I couldn't use GPUs on second node. Everytime GROMACS uses GPUs on first 
node only and fails to use GPUs on second node.

The command I used was,

mpirun -np 4  ${GROMACS}/mdrun  -v -deffnm $configfile

and please find the log file in attachment (em.log) . You can see that GROMACS 
detects only two GPUs on first node and then crashes (it is obvious as MPI 
ranks is not same as no. of gpus per node). Main thing here to note down is 
only two GPUs were detected on first node I used.


but when I tried with,

mpirun -np 4  ${GROMACS}/mdrun -gpu_id 0011 -v -deffnm $configfile

This time job completed successfully but used GPUs on first node only. please 
find logfie in attachments (em2.log)
 
Likewise, I tried with,

mpirun -np 2  ${GROMACS}/mdrun -v -deffnm $configfile
mpirun -np 2  ${GROMACS}/mdrun -gpu_id 01 -v -deffnm $configfile

Job ran successfully but couldn't use GPUs on second node.

Each node is having 2 GPUs cards. With that configuration please let me how to 
launch job on two nodes.

Thank you.

-Jignesh



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Szilárd Páll 
[pall.szil...@gmail.com]
Sent: Thursday, November 14, 2013 2:42 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] GROMACS-4.6.3 CUDA version on multiple nodes each 
having 2 GPUs

Hi Jignesh,

I don't get what the issue is, you need to be more specific than
"fails" and "none of them worked." You should provide exact command
line, stderr output and log files as we can't get what exactly is the
error you are getting.

Previously you seemed to hint that you had inhomogeneous hardware
(i.e. nodes with different CPU/GPU setup), but now you're saying that
all nodes are the same - case in which it should all work just fine
with default settings!

Cheers,
--
Szilárd


On Wed, Nov 13, 2013 at 7:55 PM, Prajapati, Jigneshkumar Dahyabhai
 wrote:
> Hello,
>
> I am trying to run MPI, OpenMP and CUDA enable GROMACS 4.6.3 on nodes having 
> 12 cores (2 CPUs) and 2 GPUs (Tesla M2090) each. The problem is when I launch 
> job GROMCAS is using only GPUs on first node come across and failing to use 
> GPUs on other nodes.
>
> The command I used for two gpu enable nodes was,
>
> mpirun -np 2  mdrun -v -deffnm $configfile
>
> I tried with many other options but none of them worked. The one thing needs 
> to remember here is that on all the nodes, GPUs got id 0 and 1 so -gpu_id 
> option also didn't work.
>
> This old thread gave me some idea but I didn't understand it completely.
> http://lists.gromacs.org/pipermail/gmx-users/2013-March/079802.html
>
> Please suggests me the possible solutions for this issue.
>
> Thank you
> --Jignesh
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Re: [gmx-users] installing latest version of gromacs 4.6.3

[Luís Pereira]

Try:
source /usr/local/gromacs/bin/GMXRC

and read
4.11. Getting access to GROMACS after installation
​on page
http://www.gromacs.org/Documentation/Installation_Instructions


On 17 November 2013 09:30, vansh  wrote:

>
> hello all,
>
> I followed below mentioned instructions on how to install latest version of
> GROMACS latest version of Gromacs and installed it but now when I run
> gromacs, it is telling me gromacs is not install you can install it by
> typing "sudo apt-get install gromacs" which is just installing it from
> repository? any comments? I want to install gromacs 4.6.3 and be able to
> run
> it from anywhere in terminal.
>
> tar xfz gromacs-4.6.3.tar.gz
> cd gromacs-4.6.3
> mkdir build
> cd build
> cmake .. -DGMX_BUILD_OWN_FFTW=ON
> make
> sudo make install
>
> please help..:)
>
> -
> thanks in advance :)
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/installing-latest-version-of-gromacs-4-6-3-tp5012529.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] restart failed

[Mark Abraham]

On Sat, Nov 16, 2013 at 10:46 AM, xiao  wrote:

> Hi all gromacs users,
>
> My simulation crashed, and i try to restart it by using the following
> command:  mdrun -s topol.tpr -cpi state.cpt
>

Not using -deffnm means mdrun expects to write traj.trr, traj.xtc,
ener.edr...


> The version of the software is 4.5.4, and i got the following error:
>
>
> File appending requested, but only 1 of the 4 output files are present
> Output files present: md.log
> output files nor present or named differentaly: md.trr md.xtc md.edr
>

... which is not what it wrote last time. Do the restart the same way as
the original run.

Mark


>
> I checked the md.trr md.xtc md.edr, and they are in the same directory. I
> have no idea why the software comlained it?
>
> Any idea is appreciated
>
> Best wishes
>
> Fugui
>
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Re: [gmx-users] GROMACS-4.6.3 CUDA version on multiple nodes each having 2 GPUs

[Prajapati, Jigneshkumar Dahyabhai]

Hi Carsten,

Thanks for reply. Everything is working fine on single node. The problem starts 
when I move to two nodes.

I have tried with the option that you have mentioned earlier and this is the 
error I got ,
mpirun -np 4 mdrun

mismatching number of PP MPI processes and GPUs per node.
mdrun was started with 4 PP MPI processes per node, but only 2 GPUs were 
detected.

Likewise, I have tried many options and on many occasions job runs but without 
using GPUs on second node . More specifically, my problem is when I use two 
nodes each having two GPU cards, GROMACS detects GPUs on first node only. It 
fails to detect GPU cards on second node (check the em.log file in 
attachments). I am not sure what is the reason. Please let me know if I could 
try something else.

Thank you.

-Jignesh






From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Carsten 
Kutzner [ckut...@gwdg.de]
Sent: Thursday, November 14, 2013 10:54 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] GROMACS-4.6.3 CUDA version on multiple nodes each  
having 2 GPUs

Hi,

if you run on a single node with 2 GPUs, this command line should work:

> mpirun -np 2  mdrun -v -deffnm $configfile

If you run on two nodes, try this:
mpirun -np 4 mdrun

Choosing -np equal to the total number of GPUs should work (although it might
not be the best option performance-wise).

For a better performance you can try
mpirun -np 4 mdrun -gpu_id 0011on a single node
or
mpirun -np 8 mdrun -gpu_id 0011on two nodes

Carsten


On Nov 13, 2013, at 7:55 PM, "Prajapati, Jigneshkumar Dahyabhai" 
 wrote:

> Hello,
>
> I am trying to run MPI, OpenMP and CUDA enable GROMACS 4.6.3 on nodes having 
> 12 cores (2 CPUs) and 2 GPUs (Tesla M2090) each. The problem is when I launch 
> job GROMCAS is using only GPUs on first node come across and failing to use 
> GPUs on other nodes.
>
> The command I used for two gpu enable nodes was,
>
> mpirun -np 2  mdrun -v -deffnm $configfile
>
> I tried with many other options but none of them worked. The one thing needs 
> to remember here is that on all the nodes, GPUs got id 0 and 1 so -gpu_id 
> option also didn't work.
>
> This old thread gave me some idea but I didn't understand it completely.
> http://lists.gromacs.org/pipermail/gmx-users/2013-March/079802.html
>
> Please suggests me the possible solutions for this issue.
>
> Thank you
> --Jignesh
> --
> gmx-users mailing listgmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa

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Re: [gmx-users] GROMACS 4.6.4 is released

[jkrieger]

Thanks Mark.

On 14 Nov 2013, at 10:20, Mark Abraham  wrote:

> Hi,
> 
> Good question. That is our hope, from the way we have selected and
> implemented the changes in 4.6.x series. Except actual bug fixes, of
> course! The idea is that the new patch release implements the same physics,
> so a restart should be seamless. You can take any 4.6.x and restart it on a
> different number of processors and there should be no observable change
> apart from mdrun warning you that reproducibility is now even more
> impossible. Restarting with a later 4.6.x should work similarly smoothly.
> 
> However, it's completely infeasible for us to test all the possibilities,
> even had we the resources to attempt it. So, I would strongly encourage you
> to test that you can observe no problems before you commit to that
> strategy. As a reviewer, I would expect that you showed that changing your
> black-box method was not a change of method. Throwing away a few
> nanoseconds after the restart should be ample relaxation, if any were
> required.
> 
> Mark
> On Nov 13, 2013 6:31 PM,  wrote:
> 
>> Will a simulation from 4.6.1 continue running fine if I upgrade to 4.6.4?
>> 
>>> Hi GROMACS users,
>>> 
>>> GROMACS 4.6.4 is officially released. It contains numerous bug fixes, and
>>> some noteworthy simulation performance enhancements (particularly with
>>> GPUs!). We encourage all users to upgrade their installations from
>> earlier
>>> 4.6-era releases.
>>> 
>>> You can find the code, manual, release notes, installation instructions
>>> and
>>> test
>>> suite at the links below. Note that some tests have been added, and the
>>> manual has changed only in chapter 7 and appendix D.
>>> 
>>> ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.4.tar.gz
>>> ftp://ftp.gromacs.org/pub/manual/manual-4.6.4.pdf
>> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x#Release_notes_for_4.6.4
>>> http://www.gromacs.org/Documentation/Installation_Instructions
>>> http://gromacs.googlecode.com/files/regressiontests-4.6.4.tar.gz
>>> 
>>> Happy simulating!
>>> 
>>> The GROMACS team
>>> --
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[gmx-users] test gmx-users, please ignore

[Rossen Apostolov]

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[gmx-users] energy minimization erorr

[Archana Sonawani-Jagtap]

Hi,

I am simulating a peptide in TFE-water system. I am getting following error:
1 particles communicated to PME node 4 are more than 2/3 times the
cut-off out o f the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated.

below is my em.mdp file

integrator  = steep
emtol   = 1000.0
emstep  = 0.01
nsteps  = 5
nstlist = 1
ns_type = grid
rlist   = 1.2
coulombtype = PME
rcoloumb= 1.2
rvdw= 1.2
pbc = xyz

Please help me. Why this error has ocurred and what parameter should I
change to resolve it.
Thank you.

Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339
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[gmx-users] a query

[vsharma]

 

i have posted a problem in gronacs user forum ...but its saying that it
is not accepted by the mailing list yet.. 

althuogh i am already a subscriber to it.. 

please suggest 

-- 
VANDNA
JRF
C/O Dr. Girish Sahni
Protein Science lab
Phone No. 0172-2690830
Institurte of Microbial Technology (IMTech)
Sector -39A, Chandigarh,160036
 
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[gmx-users] can not write coordinate file when running ibi

[cqgzc]

Hi: 
When I am running the ibi procedure, I get the following error message: 
A coordinate in file conf.gro does not contain a '.' 
Additionally, I check the coordinate file of confout.gro in step_001. It
showed that 'nan' symbol appeared in confout.gro. Just like:
856
1RDXRDX1 nan nan-nan nan nan-nan
2RDXRDX2 nan nan-nan nan nan-nan
3RDXRDX3 nan nan-nan nan nan-nan
4RDXRDX4 nan nan-nan nan nan-nan
5RDXRDX5 nan nan-nan nan nan-nan
6RDXRDX6 nan nan-nan nan nan-nan
7RDXRDX7 nan nan-nan nan nan-nan
What is wrong with this? How can I fix it? I am very appreciating for
anyone's help. 
Best Wishes! 
Zhicheng Guo

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[gmx-users] Cannot write trajectory frame; maybe you are out of disk space?

[vansh]

dear all,
i am getting following error on giving command:  mdrun -deffnm nvt -v -nt 8
File input/output error:
Cannot write trajectory frame; maybe you are out of disk space?

i have gromacs 4.6.4 version, 12.04 ubuntu, 7.9GiB memory and 976 GB Disk
space, i am simulating 414aa long protein for 10ns.

any help 

-
thanks in advance :)
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Re: [gmx-users] help about logfile

[cqgzc]

Hi Justin:
Thanks for your reply.
I checked the initial setting and the output file about simulation control
(mdout.mdp and .log file) and found that it's ok. There are some strange
results related to sample frequency (Statistics over *** steps using ***
frames in .log file) as described below:
 Statistics over 101 steps using 40001 frames
where,
nsteps=10,dt=0.001,nstlog=40,nstvout=40,nstxtcout=40,nstcalcenergy=50,nstenergy
=100
nstlist=10
Statistics over 6001 steps using 481 frames
where,
nsteps=6000,dt=0.001,nstlog=15,nstvout=15,nstxtcout=15,nstcalcenergy=50,nstenergy=100
nstlist=10
Specially, when
nsteps=6000,dt=0.001,nstlog=50,nstvout=50,nstxtcout=50,nstcalcenergy=100,nstenergy=100
nstlist=10
It presented the following information: 
   Statistics over 6001 steps using 121 frames
Therefore, I really want to know how to control the sample frequency.


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[gmx-users] Average number of salt bridge

[bharat gupta]

Hi,

I want to calculate the average number of salt bridge interactions between
two residues. I used g_saltbr it gives the details for all the residues.
Using g_dist I calculated the distance between the charged group of those
two residues, but I want a number for salt-bridges like g_hbond gives ??

Regards

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[gmx-users] Replicating triclinic unit cells

[Eudes Fileti]

Hi GMX users
I need replicate a triclinic unit cell. However, both
genconf and topotools (VMD plugin) generate only
orthorrombic cells. Anyone knows some free software
or script to do that?
eef
___
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Instituto de Ciência e Tecnologia da UNIFESP
Rua Talim, 330, São José dos Campos - SP
Página: sites.google.com/site/fileti/
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[gmx-users] how to pull both side

[Tom]

Dear All,

Can gromacs pull both sides (end) of a body way?
for example pulling two end of a cylinder unitl it breaks.

I knew Gromacs can pull two bodies (A and B) objects away.

Can someone inform about this functionality of pulling (both
sides/end of a same body)?

Thanks a lot!

Thomas
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[gmx-users] installing latest version of gromacs 4.6.3

[vansh]

hello all,

I followed below mentioned instructions on how to install latest version of
GROMACS latest version of Gromacs and installed it but now when I run
gromacs, it is telling me gromacs is not install you can install it by
typing "sudo apt-get install gromacs" which is just installing it from
repository? any comments? I want to install gromacs 4.6.3 and be able to run
it from anywhere in terminal.

tar xfz gromacs-4.6.3.tar.gz
cd gromacs-4.6.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON
make
sudo make install

please help..:)

-
thanks in advance :)
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[gmx-users] membrane protein tutorial

[leila karami]

Dear JustinI am using your tutorial (membrane protein) for my system.I
inserted my peptid into lipid bilayer. Now I want to solvate withwater using
genbox tool.To remove those water molecules are into lipid bilayer, I want
to usekeepbyz.pl script by Chris Neale. In step 4 of this script:4. use vi
to edit keepbyz.pl   - upperz and lowerz variables as you please   - sol to
the name of your solvent moleculeHow to select upperz and lowerz? Based on
what criterion?If I want to have z vector = 9 nm after solvation, which
value ofupperz and lowerz are appropriate?If I use another way, only
reduction of the value of C from0.15 to 0.375 in vdwradii.dat file is
enough?Best wishes.

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[gmx-users] failed restart

[xiao]

Hi all gromacs users,
My simulation crashed, and i try to restart it by using the following command: 
mdrun -s topol.tpr -cpi state.cpt
The version of the software is 4.5.4, and i got the following error:
File appending requested, but only 1 of the 4 output files are present
Output files present: md.log
output files nor present or named differentaly: md.trr md.xtc md.edr
I checked the md.trr md.xtc md.edr, and they are in the same directory. I have 
no idea why the software comlained it?
Any idea is appreciated
Best wishes
Fugui
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[gmx-users] restart failed

[xiao]

Hi all gromacs users,
 
My simulation crashed, and i try to restart it by using the following command:  
mdrun -s topol.tpr -cpi state.cpt
The version of the software is 4.5.4, and i got the following error:
 
 
File appending requested, but only 1 of the 4 output files are present
Output files present: md.log
output files nor present or named differentaly: md.trr md.xtc md.edr
 
I checked the md.trr md.xtc md.edr, and they are in the same directory. I have 
no idea why the software comlained it?
 
Any idea is appreciated
 
Best wishes
 
Fugui
 
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[gmx-users] Fwd: remd

[Shine A]

sir,

 I have a basic doubt about remd simulation. In remd is it possible to
run 16 replicas in 8 processors?
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Re: [gmx-users] RF0 and g_energy

[Williams Ernesto Miranda Delgado]

Hello
I made a rerun on a MD simulation using Reaction-Field-zero for
electrostatics. When I analyze the *.edr file with g_energy, there appears
Coul-SR and Coul-14. How can I get the Coulomb long range term? This is
very important for making LIE calculations.
I used AMBER99SB FF and
rlist = 1.2
rcoul = 0.9
coultype = Reaction-Field-zero
vdw = cut-off
rvdw = 1.4
Are these parameters ok?
Thank you
Williams



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[gmx-users] Windows/x64, VCVS2012 compiled, crash on checkpoint writing

[Mirco Wahab]

Gromacs 4.6.4 compiles (and links) perfectly w/VS2012
and nvcc from CUDA 5.5 on windows/x64
(MSVC 2012 Version 11.0.60610.01 Update 3).

But -- when compiled with VS2012 (because of linking
against CUDA 5.5 is only possible then - in contrast
to VS2010), mdrun crashes on writing the checkpoint file.

This will not happen when compiling with VS2010
(but this exludes using of CUDA 5.5, only 5.0 is
supported).

I did set up a debugging session in VS2012 in order
to determine the exception location (see below, on
entry into the named function). mdrun has been compiled
as "Release w/DebugInfo".

(This has been possibly also been a problem in 4.6.3, iirc.)


- d:\libsrc\gromacs\gromacs-4.6.4\src\gmxlib\gmxfio.c 


/* internal variant of get_file_md5 that operates on a locked file */
static int gmx_fio_int_get_file_md5(t_fileio *fio, gmx_off_t offset,
unsigned char digest[])
{
7FF7B25B74C0  mov qword ptr [state],rbx
7FF7B25B74C5  pushrbp
7FF7B25B74C6  pushrsi
7FF7B25B74C7  pushrdi
7FF7B25B74C8  mov eax,100090h

7FF7B25B74CD  call__chkstk (07FF7B28B4160h)  <== exception

7FF7B25B74D2  sub rsp,rax
7FF7B25B74D5  mov rax,qword ptr [__security_cookie 
(07FF7B29963E0h)]

7FF7B25B74DC  xor rax,rsp
7FF7B25B74DF  mov qword ptr [rsp+100080h],rax
7FF7B25B74E7  mov rsi,rdx
/*1MB: large size important to catch almost identical files */
#define CPT_CHK_LEN  1048576
md5_state_t   state;
unsigned char buf[CPT_CHK_LEN];
gmx_off_t read_len;
gmx_off_t seek_offset;
int   ret = -1;

seek_offset = offset - CPT_CHK_LEN;
if (seek_offset < 0)
7FF7B25B74EA  xor eax,eax
7FF7B25B74EC  add rdx,0FFF0h
7FF7B25B74F3  cmovs   rdx,rax
7FF7B25B74F7  mov rdi,rcx
{
--

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[gmx-users] about using do_dssp for a few residues

[jianqing]

Dear all,

I was playing "do_dssp" command in the last a few days. 

If I want to know the secondary structures of all the residues on the
protein over the trajectory, everything seems good! However, the obtained
picture (ss.xpm->ss.eps) is obviously too colourful, as all the residues are
shown on there. Somehow, for my project, I am actually only interested in
watching a few key residues. 

I therefore used the index file to select a few residues that I am
interested, and do the same analysis using "do_dssp -s md.tpr -f md.pdb -n
index.ndx". I found the secondary structure of the selected residues are
always in "Coil" status, which is not consistent with the results obtained
by checking the entire protein. 

I then did the tests to select 1-10 residues, 1-100 residues and 1-200
residues, and the results were different. The only reasonable possibility
that I can think of is that the "do_dssp" only checks the selected residues
and assumes the rest of the protein do not exist  

I was wondering whether my understanding is correct. And if this is the
case, how can I calculate the secondary structures of a few residues over
time (without manually modifying the ss.xpm file) ?

Thanks for any help!

Regards,

Jianqing


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[gmx-users] membrane protein tutorial

[leila karami]

Dear Justin

I am using your tutorial (membrane protein) for my system.

I inserted my peptid into lipid bilayer. Now I want to solvate with
water using genbox tool.
To remove those water molecules are into lipid bilayer, I want to use
keepbyz.pl script by Chris Neale. In step 4 of this script:

4. use vi to edit keepbyz.pl
   - upperz and lowerz variables as you please
   - sol to the name of your solvent molecule

How to select upperz and lowerz? Based on what criterion?
If I want to have z vector = 9 nm after solvation, which value of
upperz and lowerz are appropriate?

If I use another way, only reduction of the value of C from
0.15 to 0.375 in vdwradii.dat file is enough?

Best wishes.
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Re: [gmx-users] How to construct mixed lipid bilayer (Björn Sommer)

[Björn Sommer]

Am 13.11.2013 14:51, schrieb gmx-users-requ...@gromacs.org:

Message: 4
Date: Wed, 13 Nov 2013 18:44:08 +0530
From: Nikhil Agrawal
Subject: [gmx-users] How to construct mixed lipid bilayer
To:gmx-us...@gromacs.org
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1

Dear All,

can anyone tell me how to construct mixed lipid bilayer in gromacs

id possible also provide me the command to construct the mixed bilayer


Thanks in advance

Nikhil


Dear Nikhil,

especially for heterogeneous bilayers our MembraneEditor was developed, 
you can download it here:


http://Cm2.CELLmicrocosmos.org

It is Java Webstart, so it is quite easy to use and install, but you can 
also download the source code in the forum.


Here you find some videos about how to use it:

http://cellmicrocosmos.org/index.php/videos

We also use it with Gromacs. There is no pre-euqilibration done in the 
MembraneEditor. But we never needed it, because the equilibration with 
Gromacs works very good.


If you have further question, just let me know. A new version with a 
number of improvements is coming during the next month!


Best wishes,
Björn
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[gmx-users] test 2, please ignore

[Rossen Apostolov]

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[gmx-users] Average number of salt bridge

[bharat gupta]

Hi,

How can I calculate the average number of salt bridges between two residues
during the entire simulation ??...

Thanks
---
Bharat
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[gmx-users] g_select

[SEMRAN İPEK]

Dear gromacs users;

I have been trying to find out the waters close to certain residue. Here is
my selection dat:

waterO = name "OW";
close = waterO and within 0.35 of resnr 334;
close


**
I have been using the command of "g_select -f md_30.xtc -b 3 -e 3
 -s md_30.gro -oi index.dat -sf selection.dat"

Somehow the code sometimes finds the waters within 0.35 nm of residue  and
sometimes finds the waters too far away from protein (30 nm away .)



Could you please guide me along the process for g_select?


Best Regards;
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[gmx-users] about using do_dssp for a few residues

[Xu, Jianqing]

Dear all,

I was playing "do_dssp" command in the last a few days.

If I want to know the secondary structures of all the residues on the protein 
over the trajectory, everything seems good! However, the obtained picture 
(ss.xpm->ss.eps) is obviously too colourful, as all the residues are shown on 
there. Somehow, for my project, I am actually only interested in watching a few 
key residues.

I therefore used the index file to select a few residues that I am interested, 
and do the same analysis using "do_dssp -s md.tpr -f md.pdb -n index.ndx". I 
found the secondary structure of the selected residues are always in "Coil" 
status, which is not consistent with the results obtained by checking the 
entire protein.

I then did the tests to select 1-10 residues, 1-100 residues and 1-200 
residues, and the results were different. The only reasonable possibility that 
I can think of is that the "do_dssp" only checks the selected residues and 
assumes the rest of the protein do not exist 

I was wondering whether my understanding is correct. And if this is the case, 
how can I calculate the secondary structures of a few residues over time 
(without manually modifying the ss.xpm file) ?

Thanks for any help!

Regards,

Jianqing


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[gmx-users] Average number of salt bridge

[bharat gupta]

Hi,

How can I calculate the average number of salt bridges between two residues
during the entire simulation ??...

Thanks
---
Bharat
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[gmx-users] gmx to amber

[kiana moghaddam]

Dear GMX Users

I want to access gmxtoamber script to convert gromacs output to amber. 
Could anyone give me this script?

Best Regards
Kiana
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[gmx-users] error with make install command

[vansh]

make installcommand gave following error output output:



[  0%] Building NVCC (Device) object
src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o
cc: error trying to exec 'cc1plus': execvp: No such file or directory
CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:206 (message):
  Error generating
 
/home/vansh/Downloads/gromacs-4.6.3/build-cmake/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o


make[2]: ***
[src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o]
Error 1
make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2
make: *** [all] Error 2


-
thanks in advance :)
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Re: [gmx-users] GROMACS-4.6.3 CUDA version on multiple nodes each having 2 GPUs

[Szilárd Páll]

Hi Jignesh,

I don't get what the issue is, you need to be more specific than
"fails" and "none of them worked." You should provide exact command
line, stderr output and log files as we can't get what exactly is the
error you are getting.

Previously you seemed to hint that you had inhomogeneous hardware
(i.e. nodes with different CPU/GPU setup), but now you're saying that
all nodes are the same - case in which it should all work just fine
with default settings!

Cheers,
--
Szilárd


On Wed, Nov 13, 2013 at 7:55 PM, Prajapati, Jigneshkumar Dahyabhai
 wrote:
> Hello,
>
> I am trying to run MPI, OpenMP and CUDA enable GROMACS 4.6.3 on nodes having 
> 12 cores (2 CPUs) and 2 GPUs (Tesla M2090) each. The problem is when I launch 
> job GROMCAS is using only GPUs on first node come across and failing to use 
> GPUs on other nodes.
>
> The command I used for two gpu enable nodes was,
>
> mpirun -np 2  mdrun -v -deffnm $configfile
>
> I tried with many other options but none of them worked. The one thing needs 
> to remember here is that on all the nodes, GPUs got id 0 and 1 so -gpu_id 
> option also didn't work.
>
> This old thread gave me some idea but I didn't understand it completely.
> http://lists.gromacs.org/pipermail/gmx-users/2013-March/079802.html
>
> Please suggests me the possible solutions for this issue.
>
> Thank you
> --Jignesh
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Re: [gmx-users] GROMACS-4.6.3 CUDA version on multiple nodes each having 2 GPUs

[Carsten Kutzner]

Hi,

if you run on a single node with 2 GPUs, this command line should work:

> mpirun -np 2  mdrun -v -deffnm $configfile

If you run on two nodes, try this:
mpirun -np 4 mdrun

Choosing -np equal to the total number of GPUs should work (although it might
not be the best option performance-wise).

For a better performance you can try
mpirun -np 4 mdrun -gpu_id 0011on a single node
or
mpirun -np 8 mdrun -gpu_id 0011on two nodes

Carsten


On Nov 13, 2013, at 7:55 PM, "Prajapati, Jigneshkumar Dahyabhai" 
 wrote:

> Hello,
> 
> I am trying to run MPI, OpenMP and CUDA enable GROMACS 4.6.3 on nodes having 
> 12 cores (2 CPUs) and 2 GPUs (Tesla M2090) each. The problem is when I launch 
> job GROMCAS is using only GPUs on first node come across and failing to use 
> GPUs on other nodes.
> 
> The command I used for two gpu enable nodes was,
> 
> mpirun -np 2  mdrun -v -deffnm $configfile
> 
> I tried with many other options but none of them worked. The one thing needs 
> to remember here is that on all the nodes, GPUs got id 0 and 1 so -gpu_id 
> option also didn't work.
> 
> This old thread gave me some idea but I didn't understand it completely.
> http://lists.gromacs.org/pipermail/gmx-users/2013-March/079802.html
> 
> Please suggests me the possible solutions for this issue.
> 
> Thank you
> --Jignesh
> -- 
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--
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Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa

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[gmx-users] installation error : mpi compiler not found

[vansh]

while installing gromacs ..i gave following command:

 cmake .. -DGMX_GPU=ON -DGMX_MPI=ON
-DCMAKE_INSTALL_PREFIX=/home/marydoe/programs

to build with GPUs, MPI and install in a custom location.



error :
CMake Warning at cmake/gmxGetCompilerInfo.cmake:90 (message):
  The version of the C and C++ compilers does not match.  Note that mixing
  different C/C++ compilers can cause problems!
Call Stack (most recent call first):
  CMakeLists.txt:240 (get_compiler_version)


-- Could NOT find MPI_C (missing:  MPI_C_LIBRARIES MPI_C_INCLUDE_PATH) 
-- Could NOT find MPI_CXX (missing:  MPI_CXX_LIBRARIES MPI_CXX_INCLUDE_PATH) 
CMake Error at cmake/gmxManageMPI.cmake:161 (message):
  MPI support requested, but no MPI compiler found.  Either set the
  C-compiler (CMAKE_C_COMPILER) to the MPI compiler (often called mpicc), or
  set the variables reported missing for MPI_C above.
Call Stack (most recent call first):
  CMakeLists.txt:507 (include)


-
thanks in advance :)
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Re: [gmx-users] GROMACS 4.6.4 is released

[Mark Abraham]

Hi,

Good question. That is our hope, from the way we have selected and
implemented the changes in 4.6.x series. Except actual bug fixes, of
course! The idea is that the new patch release implements the same physics,
so a restart should be seamless. You can take any 4.6.x and restart it on a
different number of processors and there should be no observable change
apart from mdrun warning you that reproducibility is now even more
impossible. Restarting with a later 4.6.x should work similarly smoothly.

However, it's completely infeasible for us to test all the possibilities,
even had we the resources to attempt it. So, I would strongly encourage you
to test that you can observe no problems before you commit to that
strategy. As a reviewer, I would expect that you showed that changing your
black-box method was not a change of method. Throwing away a few
nanoseconds after the restart should be ample relaxation, if any were
required.

Mark
On Nov 13, 2013 6:31 PM,  wrote:

> Will a simulation from 4.6.1 continue running fine if I upgrade to 4.6.4?
>
> > Hi GROMACS users,
> >
> > GROMACS 4.6.4 is officially released. It contains numerous bug fixes, and
> > some noteworthy simulation performance enhancements (particularly with
> > GPUs!). We encourage all users to upgrade their installations from
> earlier
> > 4.6-era releases.
> >
> > You can find the code, manual, release notes, installation instructions
> > and
> > test
> > suite at the links below. Note that some tests have been added, and the
> > manual has changed only in chapter 7 and appendix D.
> >
> > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.4.tar.gz
> > ftp://ftp.gromacs.org/pub/manual/manual-4.6.4.pdf
> >
> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x#Release_notes_for_4.6.4
> > http://www.gromacs.org/Documentation/Installation_Instructions
> > http://gromacs.googlecode.com/files/regressiontests-4.6.4.tar.gz
> >
> > Happy simulating!
> >
> > The GROMACS team
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>
>
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Re: [gmx-users] remd

[Mark Abraham]

Yes, just tell your MPI setup to do that. Performance will degrade, and
mdrun will complain that it can't set processor affinities, which is fine
for your purpose.

Mark
On Nov 14, 2013 7:06 AM, "Shine A"  wrote:

> sir,
>
>  I have a basic doubt about remd simulation. In remd is it possible to
> run 16 replicas in 8 processors?
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Re: [gmx-users] Recompile Gromacs 4.6.3

[Jheng Wei Li]

Hello, all
Could any one help me on this problem?
I intend to make some modification on minimize.c in mdlib.
Do I need to do "cmake make make install" all over again?
Or is there a quick way for recompiling?

Thanks for any tips.

JhengWei Li
Institute of Atomic and Molecular Sciences,
Academia Sinica, Taipei 106, Taiwan


On Wed, Nov 13, 2013 at 9:47 PM, Jheng Wei Li  wrote:

> Hello, all
> I intend to make some modification on minimize.c in mdlib.
> Do I need to do "cmake make make install" all over again?
> Or is there a quick way for recompiling?
>
> Thanks for any tips.
>
> JhengWei Li
> Institute of Atomic and Molecular Sciences,
> Academia Sinica, Taipei 106, Taiwan
>
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Re: [gmx-users] Recompile Gromacs 4.6.3

[Jheng Wei Li]

Sorry , somehow I didn't receive the reply message on mailbox
And thanks for Mark's help!!
JhengWei Li
Institute of Atomic and Molecular Sciences,
Academia Sinica, Taipei 106, Taiwan


On Thu, Nov 14, 2013 at 6:02 PM, Jheng Wei Li  wrote:

> Hello, all
> Could any one help me on this problem?
> I intend to make some modification on minimize.c in mdlib.
> Do I need to do "cmake make make install" all over again?
> Or is there a quick way for recompiling?
>
> Thanks for any tips.
>
> JhengWei Li
> Institute of Atomic and Molecular Sciences,
> Academia Sinica, Taipei 106, Taiwan
>
>
> On Wed, Nov 13, 2013 at 9:47 PM, Jheng Wei Li wrote:
>
>> Hello, all
>> I intend to make some modification on minimize.c in mdlib.
>> Do I need to do "cmake make make install" all over again?
>> Or is there a quick way for recompiling?
>>
>> Thanks for any tips.
>>
>> JhengWei Li
>> Institute of Atomic and Molecular Sciences,
>> Academia Sinica, Taipei 106, Taiwan
>>
>
>
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Re: [gmx-users] remd

[Justin Lemkul]

On 11/14/13 1:05 AM, Shine A wrote:

sir,

  I have a basic doubt about remd simulation. In remd is it possible to
run 16 replicas in 8 processors?



No.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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