Re: [gmx-users] which source file is handling for writing distance restraint potential energy to edr file?

[Mark Abraham]

Hi,

There isn't a single place that handles this, and you don't want to get
involved ;-) What you can do is get the forces via a
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy using .tpr
files that do and do not have the restraints, read the two sets of forces
into some program you write, and subtract the results.

Mark

On Mon, Feb 15, 2016 at 8:45 AM Yuno Lee  wrote:

> Dear Gromacs users,
>
> Is there someone that can help me to find out
> which source file handles writing distance restraint potential energy to
> edr file?
>
> I want to extract the restrained force instead of potential energy through
> changing the source code.
>
>
> Any help would be appreciated.
>
> --
> Thanks & Regards,
>
>
> Yuno Lee, Ph.D.
> ---
>
> Theoretical and Computational Biophysics Lab (Prof. Changbong Hyeon)
> School of Computational Sciences, Korea Institute for Advanced Study (KIAS)
> 85 Hoegiro, Dongdaemun-gu, Seoul 130-722, Korea
> Tel: 82-2-958-3889, Mobile : 82-10-9396-2729
> Fax: 82-2-958-3820
> E-mail : yunol...@kias.re.kr; *yunol...@gmail.com *
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[gmx-users] which source file is handling for writing distance restraint potential energy to edr file?

[Yuno Lee]

Dear Gromacs users,

Is there someone that can help me to find out
which source file handles writing distance restraint potential energy to
edr file?

I want to extract the restrained force instead of potential energy through
changing the source code.


Any help would be appreciated.

-- 
Thanks & Regards,


Yuno Lee, Ph.D.
---

Theoretical and Computational Biophysics Lab (Prof. Changbong Hyeon)
School of Computational Sciences, Korea Institute for Advanced Study (KIAS)
85 Hoegiro, Dongdaemun-gu, Seoul 130-722, Korea
Tel: 82-2-958-3889, Mobile : 82-10-9396-2729
Fax: 82-2-958-3820
E-mail : yunol...@kias.re.kr; *yunol...@gmail.com *
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[gmx-users] genebox and solvate command

[Mehreen Jan]

 when I have run the genbox command, it has shown that "This tool has been 
removed from Gromacs
5.0. Please see
http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0
for ideas how to perform the same tasks with the new tools."


In gromacs site, it is written that
genbox

This tool has been split to gmx solvate and gmx insert-molecules.
gmx

for solvate command:
solvate -cp *.pdb -cs spc216.gro -p topol.top -o *.pdb

 error:
undefined solute box
create one with gmx editconf or give expicit -box command line option??


what about gene box???


with "gmx help solvate"  and "gmx help
insert-molecules it is not clear what should i do???
what command are used???

thank you
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Re: [gmx-users] DSSP secondary structure

[mohammad r]

I changed and reduced the ratio but the xpm file was not changed at all.
 

On Sunday, February 14, 2016 5:05 PM, Justin Lemkul  wrote:
 

 

On 2/14/16 1:54 AM, mohammad r wrote:
> Thank you Justin,
>
> I used xpm2ps command with below m2p file but the resolution was not changed.
> I've attached the xpm file, even the legend can't be seen.
> is there anyway to get the result file in pdf format?
>
> m2p file (I found it in the gromacs website):
>

> xbox = 2.0 ; x‐size of a matrix element
> ybox = 2.0 ; y‐size of a matrix element

You have a rectangular matrix, with the x-dimension being much longer than the 
y-dimension.  If you set these two values to be the same, what happens to the 
size of the rectangle?  It gets uniformly scaled.  So naturally that 
accomplishes nothing.  What you need to do is reduce the ratio of xbox/ybox.

-Justin

-- 
==

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

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

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

==
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[gmx-users] How I merge all .tpr files

[Abid Channa]

Dear Gromacs users,
I have run 50 ns simulation job in five steps. Now I am going to analyze  
energy, rmsd, rmsf etc of these simulations. I have merged all files like .gro, 
.xtc, .edr etc. But I want to merge all extend tpr files in one file for 
analyzing purpose. Is there any command to merge all .tpr files in single file. 
or any other way to analyze these tpr files kindly give your suggestions.
Regards,



Abid Ali Channa,
Junior Research Fellow,
Lab No.  P-133, Computational Chemistry Unit,
 Dr .Panjwani Center for Molecular Medicine and Drug Research (PCMD),
 International Center for Chemical and Biological Sciences  (ICCBS),
 University of Karachi-75270.Karachi-Pakistan.UAN # (92-21) 111-222-292 Ext. 
(309)
 Cell # +923013553051.
http://www.iccs.edu/
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Re: [gmx-users] fatal error trying to simulate glycosylated proteins

[Justin Lemkul]

On 2/14/16 8:19 PM, David Newman wrote:

Hi,

I'm trying to simulate the dynamics of glycosylated proteins using gromacs 
4.6.5 and have acquired forcefield parameters from PTM-Vienna (ffG45a3(v1.6) 
and ffG54a7(v1.7)) and CHARMM-GUI (36-jun2015) that supposedly allow for 
analysis of PTMs but both result in a fatal error when trying to run pdb2gmx 
-failing to recognise the identifier NAG - is there an alternative identifier I 
can use?



I can't speak to the GROMOS parameter sets, but the CHARMM-GUI output should 
include everything you need - force field, topology, coordinates, and .mdp files 
so there is no need to run pdb2gmx (because it won't handle glycosylations 
nicely and residue names may mismatch or not exist).


-Justin

--
==

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

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

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

==
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[gmx-users] fatal error trying to simulate glycosylated proteins

[David Newman]

Hi,

I'm trying to simulate the dynamics of glycosylated proteins using gromacs 
4.6.5 and have acquired forcefield parameters from PTM-Vienna (ffG45a3(v1.6) 
and ffG54a7(v1.7)) and CHARMM-GUI (36-jun2015) that supposedly allow for 
analysis of PTMs but both result in a fatal error when trying to run pdb2gmx 
-failing to recognise the identifier NAG - is there an alternative identifier I 
can use?

Thanks,

David
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[gmx-users] gmx cluster

[sun]

Hi Everyone
I performed a 10ns MD using Gromos 43a1 ff and obtained frames at 10ps 
interval. However, When i gave gmx cluster command, I obatined 661 clusters. 
Does this indicate my proteini is not stable? However When i viewed trajectory 
in VMD, it seems good with least fluctuations in structure of protein and RMSD 
plot is also not bad. When again, i performed 10ms Md of protein-ligand, the 
number of clusters increased to 710. Is that ok?  

With Regards
Suniba

Sent from my iPhone
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Re: [gmx-users] Simulation Terminated on Clusters Due to "cannot rename checkpoint file"

[Mark Abraham]

Hi,

GROMACS works correctly if you have permissions to read and write and
enough space to do so. But I expect that you can't try to run from $WORK
using mdrun -cpi $HOME/old.cpt if $HOME is full.

I suggest you consult the docs for the cluster, and consult your sysadmins
for any help with your script.

Mark

On Sun, Feb 14, 2016 at 7:17 PM Ray Chao  wrote:

> Hi, Mark,
>
> Thank you for your response. I am not sure if this is the right way to
> reply, because I cannot see the content of gmx maillist emails.
>
> I am running in my own space. Here is the story. Everybody has a $HOME and
> $WORK directory on the cluster. The $HOME is for permanent storage with
> 100GB disk space and $WORK is for temporary storage with 1TB storage.
> Initially I was running my case on $HOME. Since the files begin to pile up,
> the space is running out, I turned to the $WORK directory. At that time, I
> began to receive such an error message. Even I then move my cases back to
> $HOME, it did not work either.
>
> Best regards,
> Lei Zhao
> Ph.D Student in Mechanical Engineering, Virginia Tech
> Mobile:+1-540-750-9042
> --
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Re: [gmx-users] Simulation Terminated on Clusters Due to "cannot rename checkpoint file"

[Ray Chao]

Hi, Mark,

Thank you for your response. I am not sure if this is the right way to
reply, because I cannot see the content of gmx maillist emails.

I am running in my own space. Here is the story. Everybody has a $HOME and
$WORK directory on the cluster. The $HOME is for permanent storage with
100GB disk space and $WORK is for temporary storage with 1TB storage.
Initially I was running my case on $HOME. Since the files begin to pile up,
the space is running out, I turned to the $WORK directory. At that time, I
began to receive such an error message. Even I then move my cases back to
$HOME, it did not work either.

Best regards,
Lei Zhao
Ph.D Student in Mechanical Engineering, Virginia Tech
Mobile:+1-540-750-9042
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Re: [gmx-users] Porting to Gromacs of Parmbsc1

[Mark Abraham]

Hi,

Nobody's working on it to my knowledge, but if a forcefield has been
published, seems likely to be of use to multiple people, and a validation
script can show it works correctly with respect to the reference
implementation, then we'll consider it for inclusion in GROMACS.

Mark

On Sun, 14 Feb 2016 14:39 Sarath Chandra 
wrote:

> I wish to use Parmbsc1 for DNA simulations. Are there any timelines to port
> Parmbsc1 into Gromacs along with amber14sb?
>
> Regards,
>
> Sarath
> --
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Re: [gmx-users] Installation problem

[Mark Abraham]

Hi,

As you have read in the install guide (hint, hint) CUDA and OpenCL support
are mutually exclusive. Your second attempt was clearly run in the same
build directory, so you have not changed your previous choice where OpenCL
was on. Either turn it off, change build directory, or clear the contents
of the build directory.

Mark

On Sun, 14 Feb 2016 15:46 Prof. Eddie  wrote:

> Thanks. I thought it would be better to have ocl as well just in case.
> However, I tried you suggestion:
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON ; make
> and it still have the same error
> [100%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.c.o
> Linking CXX shared library ../../lib/libgromacs.so
> [100%] Built target libgromacs
> [100%] Building CXX object
> share/template/CMakeFiles/template.dir/template.cpp.o
> Linking CXX executable ../../bin/template
> ../../lib/libgromacs.so.1.2.0: undefined reference to
> `clEnqueueBarrierWithWaitList'
> ../../lib/libgromacs.so.1.2.0: undefined reference to
> `clEnqueueMarkerWithWaitList'
> collect2: error: ld returned 1 exit status
> make[2]: *** [bin/template] Error 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> make: *** [all] Error 2
>
> I did a make clean first and that didn't help. Thanks for continuing to
> help,
> Eddie
>
> On Sun, Feb 14, 2016 at 7:41 AM, Dr. Eddie  wrote:
>
> > Thanks. I thought it would be better to have ocl as well just in case.
> > However, I tried you suggestion:
> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON ; make
> > and it still have the same error
> > [100%] Building C object
> > src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.c.o
> > Linking CXX shared library ../../lib/libgromacs.so
> > [100%] Built target libgromacs
> > [100%] Building CXX object
> > share/template/CMakeFiles/template.dir/template.cpp.o
> > Linking CXX executable ../../bin/template
> > ../../lib/libgromacs.so.1.2.0: undefined reference to
> > `clEnqueueBarrierWithWaitList'
> > ../../lib/libgromacs.so.1.2.0: undefined reference to
> > `clEnqueueMarkerWithWaitList'
> > collect2: error: ld returned 1 exit status
> > make[2]: *** [bin/template] Error 1
> > make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> > make: *** [all] Error 2
> >
> > I did a make clean first and that didn't help.
> >
> > On Sat, Feb 13, 2016 at 12:04 PM, Nikhil Maroli 
> > wrote:
> >
> >> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> >>
> >>
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> >
> >
> > --
> > Eddie
> >
>
>
>
> --
> _
> Edward Ackad, Ph.D 
> Assistant Professor of Physics
> Computational Nanophotonics
> Southern Illinois University Edwardsville
> (618) 650-2390
> --
> Gromacs Users mailing list
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Re: [gmx-users] Installation problem

[Prof. Eddie]

Thanks. I thought it would be better to have ocl as well just in case.
However, I tried you suggestion:
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON ; make
and it still have the same error
[100%] Building C object
src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.c.o
Linking CXX shared library ../../lib/libgromacs.so
[100%] Built target libgromacs
[100%] Building CXX object
share/template/CMakeFiles/template.dir/template.cpp.o
Linking CXX executable ../../bin/template
../../lib/libgromacs.so.1.2.0: undefined reference to
`clEnqueueBarrierWithWaitList'
../../lib/libgromacs.so.1.2.0: undefined reference to
`clEnqueueMarkerWithWaitList'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2

I did a make clean first and that didn't help. Thanks for continuing to
help,
Eddie

On Sun, Feb 14, 2016 at 7:41 AM, Dr. Eddie  wrote:

> Thanks. I thought it would be better to have ocl as well just in case.
> However, I tried you suggestion:
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON ; make
> and it still have the same error
> [100%] Building C object
> src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.c.o
> Linking CXX shared library ../../lib/libgromacs.so
> [100%] Built target libgromacs
> [100%] Building CXX object
> share/template/CMakeFiles/template.dir/template.cpp.o
> Linking CXX executable ../../bin/template
> ../../lib/libgromacs.so.1.2.0: undefined reference to
> `clEnqueueBarrierWithWaitList'
> ../../lib/libgromacs.so.1.2.0: undefined reference to
> `clEnqueueMarkerWithWaitList'
> collect2: error: ld returned 1 exit status
> make[2]: *** [bin/template] Error 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> make: *** [all] Error 2
>
> I did a make clean first and that didn't help.
>
> On Sat, Feb 13, 2016 at 12:04 PM, Nikhil Maroli 
> wrote:
>
>> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>>
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>
> --
> Eddie
>



-- 
_
Edward Ackad, Ph.D 
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390
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[gmx-users] Porting to Gromacs of Parmbsc1

[Sarath Chandra]

I wish to use Parmbsc1 for DNA simulations. Are there any timelines to port
Parmbsc1 into Gromacs along with amber14sb?

Regards,

Sarath
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Re: [gmx-users] DSSP secondary structure

[Justin Lemkul]

On 2/14/16 1:54 AM, mohammad r wrote:

Thank you Justin,

I used xpm2ps command with below m2p file but the resolution was not changed.
I've attached the xpm file, even the legend can't be seen.
is there anyway to get the result file in pdf format?

m2p file (I found it in the gromacs website):




xbox = 2.0 ; x‐size of a matrix element
ybox = 2.0 ; y‐size of a matrix element


You have a rectangular matrix, with the x-dimension being much longer than the 
y-dimension.  If you set these two values to be the same, what happens to the 
size of the rectangle?  It gets uniformly scaled.  So naturally that 
accomplishes nothing.  What you need to do is reduce the ratio of xbox/ybox.


-Justin

--
==

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

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

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

==
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[gmx-users] pulling simulation

[Mehrnoosh Hazrati]

I see.

Thank you dear Justin.

Best regards,
Mehrnoosh

On Sat, Feb 13, 2016 at 6:54 PM, Mehrnoosh Hazrati <
mehrnoosh.hazr...@modares.ac.ir> wrote:

> Dear all,
>
> I'm trying to do umbrella sampling. But after running "perl distances.pl",
> I get a "summary_distances.dat file which has NO distances! Before, I get
> an error "pull reference distance for group 1 is negative" while I run
> grompp and then mdrun for pulling simulation.
>
> Below is my pull_md.mdp file.
>
> Thank you for any help and suggestion.
>
> Regards
> Mehrnoosh
>
> P.S.
> I'm using gromacs v4.5.7
>
>
> pull_md.mdp file:
>
> title   = Umbrella pulling simulation
> ; Run parameters
> integrator  = md
> dt  = 0.001
> tinit   = 0
> nsteps  = 500; 5 ns
> nstcomm = 10
> ; Output parameters
> nstxout = 1000  ; every 10 ps
> nstvout = 1000
> nstfout = 500
> nstxtcout   = 500   ; every 1 ps
> nstenergy   = 500
> ; Bond parameters
> constraint_algorithm= lincs
> constraints = all-bonds
> continuation= yes   ; continuing from NPT
> ; Single-range cutoff scheme
> nstlist = 10
> ns_type = grid
> rlist   = 1
> rcoulomb= 1
> rvdw= 1
> ; PME electrostatics parameters
> coulombtype = PME
> fourierspacing  = 0.12
> fourier_nx  = 0
> fourier_ny  = 0
> fourier_nz  = 0
> pme_order   = 4
> ewald_rtol  = 1e-5
> optimize_fft= yes
> ; Berendsen temperature coupling is on in two groups
> Tcoupl  = V-rescale
> tc_grps = DPPC  DRG  SOL
> tau_t   = 0.5   0.5  0.5
> ref_t   = 310   310  310
> ; Pressure coupling is on
> Pcoupl  = Parrinello-Rahman
> pcoupltype  = semiisotropic
> tau_p   = 2.0   2
> compressibility = 4.5e-5  4.5e-5
> ref_p   = 1.0 1.0
> refcoord_scaling = com
> ; Generate velocities is off
> gen_vel = no
> ; Periodic boundary conditions are on in all directions
> pbc = xyz
> ; Long-range dispersion correction
> DispCorr= EnerPres
> ; Pull code
> pull= umbrella
> pull_geometry   = distance
> pull_dim= N N Y
> pull_start  = yes
> pull_ngroups= 1
> pull_group0 = LIPID
> pull_group1 = DRUG
> pull_init1  =  0
> pull_rate1  = -0.01
> pull_k1 = 500 ; kJ mol^-1 nm^-2
> pull_nstxout= 1000  ; every 2 ps
> pull_nstfout= 1000  ; every 2 ps
>



-- 
**
 Mehrnoosh Kh. Hazrati 
 PhD Candidate of Physical Chemistry,Tarbiat Modares University,Tehran,
Iran 
 *** Phone : +989123436300 ***
*** Mail : mehrnoosh.hazr...@modares.ac.ir  ***
*"*
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Re: [gmx-users] Simulation Terminated on Clusters Due to "cannot rename checkpoint file"

[Mark Abraham]

Hi,

You need write permission for the folder as well. Thus, run in your own
file space.

Mark

On Sun, 14 Feb 2016 01:16 Ray Chao  wrote:

> D​ear gmx users,
>
> Just a little revision for my last question.
>
> I am running my cases on the cluster. The simulation was always terminated
> after running for a while. The error was always "
> *cannot rename checkpoint file: maybe you are out of disk space*". However,
> I have 1TB of disk
> allocation, which is enough,  and the disk is in good condition. Besides, I
> created the .top .gro .mdp files on my own workstation and also changed the
> permission from "read-only" to "read and write".  The gromacs version is
> 5.0.2 or 5.1.2 on the clusters.
>
> Is there any specific requirement about running gromacs on clusters? Your
> response is very much appreciated.​
>
> You all have a good Valentine's day.
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