date:20160421

[gmx-users] Catenation and Visualization

2016-04-21 Thread suniba

Hello everyone
I have completed two independent 100 ns simulations of two differnt proteins in 
water. One is monomer and the other is trimer. Both simulations were allowed to 
run for 50 ns intially, after visulation, trajectories were 'correct' and then 
extended the simulation to 100 ns. Now after completion and catenation, when i 
converted the .xtc into movie.pdb using trjconv, the molecule seems broken in 
all the frames and i am not able to view it in cartoon style. Moreover, when i 
load the .pdb file of monomer or trimer in Pymol, Always two files are getting 
uploaded. I dont know what is the other file but it remains 'static' when i 
play the movie. Is this visualization problem or i madd a mistake in 
catenation? Can someone plz give insight
With Regards

Sent from my iPhone
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Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

2016-04-21 Thread Justin Lemkul




On 4/21/16 4:30 PM, Pedro Lacerda wrote:

Hi Mark,

I starting converting from AMBER (according to the paper) to GROMACS and
comparing the results.

Please explain in more words what this constant of two mean or how can I
handle it. Ignoring it and just converting the units, I got these results



It's force field convention, just different notation.  Sometimes different force 
fields or programs use Rmin/2, Rmin, or sigma.  They're easily converted, e.g.:


sigma = (Rmin/2)*2*2^(-1/6)

and in GROMACS the units are nm so you need an additional multiplication by 0.1 
to convert A -> nm.



AMBER (table 2a)
Rmin/2 (Å) epsilon (kcal/mol)
Zn2+ 1.10E+00 1.25E-02
Mg2+ 7.93E-01 8.95E-01
Ca2+ 1.71E+00 4.60E-01
AMBER converted
R (nm) epsilon (kJ/mol)
Zn2+ 2.20E+01 5.23E-02
Mg2+ 1.59E+01 3.74E+00
Ca2+ 3.43E+01 1.92E+00

amber99sb-ildn.ff/ffnonbonded.itp
sigma (nm) epsilon (kJ/mol)
Zn2+ 1.96E-01 5.23E-02
Mg2+ 1.41E-01 3.74E+00
Ca2+ 3.40E-01 3.60E-01

I got exact matches for epsilon in Zn and Mg, but not for Ca.  Also the
difference on sigma was in the order Å/10, except for Zn which was
relatively significant.



See above for the proper way to convert Rmin/2 to sigma.

As for Ca, probably the parameters are coming from a different source.  I don't 
know what "Table 2a" means or what paper it's from, but you need to verify that 
the source of parameters is compatible or that you understand where differences 
are coming from.


-Justin

--
==

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

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

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

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Re: [gmx-users] Installation Problem... No command 'gmx' found

2016-04-21 Thread Md. Imrul Reza Shishir

Thanks everyone. For your quick reply and support.

On Thu, Apr 21, 2016 at 10:37 PM, Justin Lemkul  wrote:

>
>
> On 4/21/16 9:35 AM, Sotirios Dionysios I. Papadatos wrote:
>
>> Hi, in my case gmx is only needed for certain commands. For example
>> pdb2gmx is working if I use it solo, not with gmx. It's worth a shot.
>>
>>
> This is true for versions in the 5.0.x series; they can be called via gmx
> or through the old syntax without it because the commands are all installed
> as links to gmx.  In 5.1.x this will not work; gmx/gmx_mpi (depending on
> the installation) is mandatory.
>
> -Justin
>
>
> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Email
>> Gmail Pribadi 
>> Sent: Thursday, April 21, 2016 9:18 AM
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Installation Problem... No command 'gmx' found
>>
>> Hi,
>>
>> Try gmx [command] . Ex. gmx mdrun -option
>>
>> Regards,
>>
>>
>> Husen
>>
>> On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote:
>>>
>>> Hi,
>>>
>>> Try gmx_mpi.
>>>
>>> Regards
>>> Terry
>>>
>>>
>>> On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir <
 imrul.reza.shis...@gmail.com> wrote:

 Dear all user

 I install gromacs in my laptop its perfectly ok. But i have problem to
 install in my desktop there i face problem.
 In my desktop i want to compile with cuda accelerator and MPI option. I
 install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all
 this driver is ok.

 For gromacs i run this installation command.

 tar -xzvf gromacs-5.1.2.tar.gz
 cd gromacs-5.1.2.tar.gz
 mkdir build
 cd build
 CMAKE  -DGMX_BUILD_OWN_FFTW=on
 -DGMX_GPU=on
 -DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on
 make -j16
 make check
 sudo make install -j16

 source /usr/local/gromacs/bin/GMXRC

 In the installation procedure i dont find any error. All 26 test
 completed
 without error.

 But when i try to run "gmx or gmx help"

 There is error no command gmx found. I need your guidance.

 Best Regards

 --
 *Md Imrul Reza Shishir*
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> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
>
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-- 
*Md Imrul Reza Shishir*
Master Student
*Inha University*
*CRC for NanoCellulose Future Composites*
36 Getbeol-ro, Yeonsu-gu
Incheon 21999
South Korea
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[gmx-users] Volume of system

2016-04-21 Thread Sana Saeed



 hi Gmx experts
i want to calculate Volume corresponding to the one molar standard state. is 
there any tool in gromacs to do that. i read about gmx density.
Background: i have Protein-ligand complex simulation and i need to find energy 
of restraints which requires Volume.

Thanks in advance

Sana Saeed Khan,
Research Assistant
Chemoinformatics Lab
Graduate Student, MS bioinfo
Department of Bioinformatics
Soongsil University, Seoul, South Korea.
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Re: [gmx-users] gromacs 5.1.2 mdrun can't detect GPU

2016-04-21 Thread treinz



Hi Stéphane,


Did you see the following or similar output from running 
/path/to/cuda/samples/1_Utilities/deviceQuery/deviceQuery when GROMACS wasn't 
able to detect GPU?


./deviceQuery Starting...

 CUDA Device Query (Runtime API) version (CUDART static linking)

cudaGetDeviceCount returned 35
-> CUDA driver version is insufficient for CUDA runtime version
Result = FAIL


In my case this happens.


Thanks,
Tim





At 2016-04-22 05:39:08, "Téletchéa Stéphane" 
 wrote:
>Le 21/04/2016 03:54, treinz a écrit :
>> Hi,
>>
>>
>> Can you also explain why the function calls to cudaDriverGetVersion() and 
>> cudaRuntimeGetVersion() both return 0, as in
 >>CUDA driver:0.0
 >>CUDA runtime: 0.0
>> Thanks,
>> Tim
>
>Hi all,
>
>As I already posted on the list, it seems the combination of gromacs + 
>cuda is tedious,
>I had not time to dig it further, but wrote down what worked for me:
>
>http://www.steletch.org/spip.php?article89
>
>The driver version was very close from the drivers included in the 
>default ubuntu
>installation, nvidia-smi was working fine also, but gromacs was not able 
>to detect it.
>
>Using the driver from the cuda toolkit solved the problem for me.
>I only sent a mail on the mailing list, if I have time to dig further 
>I'll try to provide more
>insight and a proper bug report. Up to now you can check if the driver 
>version is the one
>expected from the cuda toolkit (nvidia-smi -a).
>
>HTH,
>
>Stéphane
>
>-- 
>Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein 
>Design In Silico
>UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes 
>cedex 03, France
>Tél : +33 251 125 636 / Fax : +33 251 125 632
>http://www.ufip.univ-nantes.fr/  -http://www.steletch.org
>
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Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

2016-04-21 Thread Pedro Lacerda

Hi Mark,

I starting converting from AMBER (according to the paper) to GROMACS and
comparing the results.

Please explain in more words what this constant of two mean or how can I
handle it. Ignoring it and just converting the units, I got these results

AMBER (table 2a)
Rmin/2 (Å) epsilon (kcal/mol)
Zn2+ 1.10E+00 1.25E-02
Mg2+ 7.93E-01 8.95E-01
Ca2+ 1.71E+00 4.60E-01
AMBER converted
R (nm) epsilon (kJ/mol)
Zn2+ 2.20E+01 5.23E-02
Mg2+ 1.59E+01 3.74E+00
Ca2+ 3.43E+01 1.92E+00

amber99sb-ildn.ff/ffnonbonded.itp
sigma (nm) epsilon (kJ/mol)
Zn2+ 1.96E-01 5.23E-02
Mg2+ 1.41E-01 3.74E+00
Ca2+ 3.40E-01 3.60E-01

I got exact matches for epsilon in Zn and Mg, but not for Ca.  Also the
difference on sigma was in the order Å/10, except for Zn which was
relatively significant.

(I'm expecting that Mailman render the table into plain text relatively
well, so if this post go with bad formatting I'll post again)

Very thanks
Pedro


2016-04-18 21:29 GMT-03:00 Mark Abraham :

> Hi,
>
> Convert the units and absorb the factor of two to the minus six. Compare
> with other ions present in both representations of such force fields.
>
> Mark
>
> On Tue, 19 Apr 2016 02:21 Pedro Lacerda  wrote:
>
> > Hi Gromacs users,
> >
> > We are planning a simulation with a metallic (fe+2) attached on the
> > protein. The parameters found in [1] cannot be directly inserted on
> > ffnonbonded.itp because equation 1 of [1] and equation 4.5 of [2] are
> > slightly different.
> >
> > Theoreticaly these Lennard-Jones parameters could be used in any PME
> based
> > force field, but it was derived and tested using the AMBER software and
> > potential, so it is our current force field of choice. In
> > amber99sb-ildn/ffnonbonded.itp the long range interactions are described
> in
> > terms of epsilon (kJ/mol) and sigma (Rmin; nm).
> >
> > Eq 1:
> >
> > Lj = 4e ((R/r)^12 - (R/r)^6)
> >
> > Eq 4.5:
> >
> > Lj = e ((R/r)^12 - 2(R/r)^6)
> >
> > Seems that Rmin values are written as Rmin/2 in AMBER files avoiding some
> > calculations to optimize the software. But this occurs at implementation
> > level and probably does not have correspondence with the paper.
> >
> > My question is how can I adapt these parameters so they can be used in
> > Gromacs?
> >
> > (Sorry about the previous email, now the title is correct)
> >
> > [1]
> > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728907/pdf/nihms481931.pdf
> >
> > [2] ftp://ftp.gromacs.org/pub/manual/manual-5.1.2.pdf
> >
> > [3] http://comments.gmane.org/gmane.science.biology.gromacs.user/82242
> >
> >
> > Cheers,
> >
> > Pedro Lacerda
> > --
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[gmx-users] vdwradii issue

2016-04-21 Thread badamkhatan togoldor

Dear Gmx-Users
Currently i'm having this kind of sticky warning when i am doing gmx solvate or 
gmx editconf (ff was charmm and oplsa). However i copied vdwradii.dat in my 
working directory, or use -vdwread flag still get this warning..Please how to 
get rid off of this Warning!   
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.
NOTE: From version 5.0 gmx uses the Van der Waals radiifrom the source below. 
This means the results may be differentcompared to previous GROMACS versions.
Please give a some help! Thanks. (Im using gromacs/5.1.1 version) 
Khatnaa 
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[gmx-users] vdwradii issue

2016-04-21 Thread badamkhatan togoldor




Dear Gmx-Users
Currently i'm having this kind of sticky warning when i am doing gmx solvate or 
gmx editconf (ff was charmm and oplsa). However i copied vdwradii.dat in my 
working directory, or use -vdwread flag still get this warning..Please how to 
get rid off of this Warning!   
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.
NOTE: From version 5.0 gmx uses the Van der Waals radiifrom the source below. 
This means the results may be differentcompared to previous GROMACS versions.
Please give a some help! Thanks. (Im using gromacs/5.1.1 version) 
Khatnaa

  
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Re: [gmx-users] gromacs 5.1.2 mdrun can't detect GPU

2016-04-21 Thread Szilárd Páll

On Thu, Apr 21, 2016 at 3:54 AM, treinz  wrote:
> Hi,
>
>
> Can you also explain why the function calls to cudaDriverGetVersion() and 
> cudaRuntimeGetVersion() both return 0, as in

Not really, but it is the normal behavior on hosts where the runtime
is not compatible with the driver or there is simply no driver
installed.

Cheers,
--
Szilárd

>>> CUDA driver:0.0
>>> CUDA runtime: 0.0
>
>
> Thanks,
> Tim
> At 2016-04-21 08:49:17, "Szilárd Páll"  wrote:
>>On Thu, Apr 21, 2016 at 12:22 AM, treinz  wrote:
>>> Hi all,
>>>
>>>
>>> I recently built 5.1.2 with GPU support and the config options are:
>>>
>>>
>>> module load cuda/7.5.18
>>> cmake .. -DCMAKE_C_COMPILER=gcc-4.9 \
>>>  -DCMAKE_CXX_COMPILER=g++-4.9 \
>>>  -DGMX_MPI=OFF \
>>>  -DGMX_THREAD_MPI=ON \
>>>  -DGMX_GPU=ON \
>>>  -DCMAKE_PREFIX_PATH=$HOME/local \
>>>  -DCMAKE_INSTALL_PREFIX=$HOME/local/gromacs/grid_frontend \
>>>  -DGMX_BUILD_OWN_FFTW=ON \
>>>  -DGMX_DEFAULT_SUFFIX=OFF \
>>>  -DGMX_BINARY_SUFFIX=_gpu \
>>>  -DGMX_LIBS_SUFFIX=_gpu
>>>
>>>
>>> and the installation was successful. But when I tried running mdrun, it 
>>> wasn't able to detect the GPU:
>>>
>>>
>>> Build OS/arch:  Linux 2.6.32-573.1.1.el6.x86_64 x86_64
>>> Build CPU vendor:   GenuineIntel
>>> Build CPU brand:Intel(R) Xeon(R) CPU E5-2620 v3 @ 2.40GHz
>>> Build CPU family:   6   Model: 63   Stepping: 2
>>> Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt 
>>> lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd 
>>> rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
>>> C compiler: /net/noble/vol1/home/dejunlin/local/bin/mpicc GNU 4.9.3
>>> C compiler flags:-march=core-avx2-Wextra 
>>> -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall 
>>> -Wno-unused -Wunused-value -Wunused-parameter  -O3 -DNDEBUG 
>>> -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds
>>> C++ compiler:   /net/noble/vol1/home/dejunlin/local/bin/mpicxx GNU 4.9.3
>>> C++ compiler flags:  -march=core-avx2-Wextra 
>>> -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function  
>>> -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds
>>> Boost version:  1.59.0 (external)
>>> CUDA compiler:  
>>> /net/gs/vol3/software/modules-sw/cuda/7.5.18/Linux/RHEL6/x86_64/bin/nvcc 
>>> nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2015 NVIDIA 
>>> Corporation;Built on Tue_Aug_11_14:27:32_CDT_2015;Cuda compilation tools, 
>>> release 7.5, V7.5.17
>>> CUDA compiler 
>>> flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_52,code=compute_52;-use_fast_math;;
>>>  
>>> ;-march=core-avx2;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds;
>>> CUDA driver:0.0
>>> CUDA runtime:   0.0
>>>
>>>
>>> NOTE: Error occurred during GPU detection:
>>>   CUDA driver version is insufficient for CUDA runtime version
>>>   Can not use GPU acceleration, will fall back to CPU kernels.
>>>
>>
>>^^^ This is the message you should be focusing on. For some reason,
>>the runtime mdrun was compiled with is incompatible with the driver.
>>This should not be the case if the driver is indeed 352.xx (which is
>>driver API v 7.5) as shown below and the runtime API v 7.5.
>>
>>> The command lines for this run is:
>>>
>>>
>>> module load cuda/7.5.18
>>> source $HOME/local/gromacs/grid_frontend/bin/GMXRC
>>> env
>>> nvidia-smi -a
>>> gmx_gpu mdrun -ntmpi 24 -ntomp 1 -gpu_id 1 -deffnm
>>
>>FYI: That's going to be inefficient, probably the worst possible
>>option in fact. Try 1-6 ranks/GPU.
>>
>>>
>>> I look at the stdout from nvidia-smi, it looks like the nvidia driver was 
>>> installed (there are 4 GPUs but I'm only showing one of them):
>>>
>>>
>>> ==NVSMI LOG==
>>>
>>>
>>> Timestamp   : Wed Apr 20 15:05:52 2016
>>> Driver Version  : 352.39
>>>
>>>
>>> Attached GPUs   : 4
>>> GPU :02:00.0
>>> Product Name: Tesla K40c
>>> Product Brand   : Tesla
>>> Display Mode: Disabled
>>> Display Active  : Disabled
>>> Persistence Mode: Disabled
>>> Accounting Mode : Disabled
>>> Accounting Mode Buffer Size : 1920
>>> Driver Model
>>> Current : N/A
>>> Pending : N/A
>>> Serial Number   : 0321715040048
>>> GPU UUID: 
>>>

Re: [gmx-users] Moving this mailing list to Discourse format

2016-04-21 Thread Hannes Loeffler

Hi Mark,

many thanks.

At the end it is really just a question if the user has flexibility
over how to visualise the communications.  I'm happy to hear that the
old-fashioned email way would still have (some) support :-)

I hope you get sufficient feedback and support from the community.

Cheers,
Hannes.


On Thu, 21 Apr 2016 08:47:56 +
Mark Abraham  wrote:

> Hi Hannes,
> 
> Yes, previous discussion has identified this as a likely key feature,
> and thanks for adding confirmation of that. Discourse can be
> integrated with functionality for replying to threads from email to
> suit people who want that kind of small change to their workflows;
> that will indeed suit simple discussions. Obviously there's
> configurable email activity digests and notifications also, which
> provide links to the forum proper.
> 
> Mark
> 
> On Thu, Apr 21, 2016 at 9:52 AM Hannes Loeffler
>  wrote:
> 
> > On Thu, 21 Apr 2016 07:11:42 +
> > Mark Abraham  wrote:
> >
> > > Hi people,
> > >
> > > As part of the new BioExcel project (http://bioexcel.eu/) that
> > > supports biomolecular research with codes including GROMACS, we're
> > > exploring migrating the gmx-users mailing list to the Discourse
> > > format. You can see an example at http://try.discourse.org! This
> > > has a number of immediate advantages, including attachments,
> > > single-click sign-up, tagging, voting and contributing to old
> > > discussions. We might also integrate features like replying to
> > > threads via email, or real-time chat. We also know such a change
> > > might be something people don't like, and we would like to get a
> > > feel for that. The community should like its forum, after
> > > all! :-) So please let us know how you feel at
> > > http://goo.gl/forms/k8lhTliffO.
> >
> > I think such a discussion would need a bit more space than just a
> > few pre-canned questions.
> >
> > I am on various mailing lists and happy with my email client as a
> > central "collector" of all those discussions.  I am personally not
> > fond of another web page interface with its very own features,
> > bells and whistles and what not, but typically unlike any other
> > existing one. And this is in essence the major shortcoming unless
> > it would be still possible to receive all messages through a
> > mailing list as it is now.
> >
> > Cheers,
> > Hannes.
> > --
> > 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.
> >

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Re: [gmx-users] Installation Problem... No command 'gmx' found

2016-04-21 Thread Justin Lemkul




On 4/21/16 9:35 AM, Sotirios Dionysios I. Papadatos wrote:

Hi, in my case gmx is only needed for certain commands. For example pdb2gmx is 
working if I use it solo, not with gmx. It's worth a shot.



This is true for versions in the 5.0.x series; they can be called via gmx or 
through the old syntax without it because the commands are all installed as 
links to gmx.  In 5.1.x this will not work; gmx/gmx_mpi (depending on the 
installation) is mandatory.


-Justin



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Email Gmail Pribadi 

Sent: Thursday, April 21, 2016 9:18 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Installation Problem... No command 'gmx' found

Hi,

Try gmx [command] . Ex. gmx mdrun -option

Regards,


Husen


On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote:

Hi,

Try gmx_mpi.

Regards
Terry



On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir 
 wrote:

Dear all user

I install gromacs in my laptop its perfectly ok. But i have problem to
install in my desktop there i face problem.
In my desktop i want to compile with cuda accelerator and MPI option. I
install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all
this driver is ok.

For gromacs i run this installation command.

tar -xzvf gromacs-5.1.2.tar.gz
cd gromacs-5.1.2.tar.gz
mkdir build
cd build
CMAKE  -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on
-DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on
make -j16
make check
sudo make install -j16

source /usr/local/gromacs/bin/GMXRC

In the installation procedure i dont find any error. All 26 test completed
without error.

But when i try to run "gmx or gmx help"

There is error no command gmx found. I need your guidance.

Best Regards

--
*Md Imrul Reza Shishir*
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--
==

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

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

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

==
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Re: [gmx-users] Installation Problem... No command 'gmx' found

2016-04-21 Thread Sotirios Dionysios I. Papadatos

Hi, in my case gmx is only needed for certain commands. For example pdb2gmx is 
working if I use it solo, not with gmx. It's worth a shot.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Email Gmail 
Pribadi 
Sent: Thursday, April 21, 2016 9:18 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Installation Problem... No command 'gmx' found

Hi,

Try gmx [command] . Ex. gmx mdrun -option

Regards,


Husen

> On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote:
>
> Hi,
>
> Try gmx_mpi.
>
> Regards
> Terry
>
>
>> On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir 
>>  wrote:
>>
>> Dear all user
>>
>> I install gromacs in my laptop its perfectly ok. But i have problem to
>> install in my desktop there i face problem.
>> In my desktop i want to compile with cuda accelerator and MPI option. I
>> install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all
>> this driver is ok.
>>
>> For gromacs i run this installation command.
>>
>> tar -xzvf gromacs-5.1.2.tar.gz
>> cd gromacs-5.1.2.tar.gz
>> mkdir build
>> cd build
>> CMAKE  -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on
>> -DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on
>> make -j16
>> make check
>> sudo make install -j16
>>
>> source /usr/local/gromacs/bin/GMXRC
>>
>> In the installation procedure i dont find any error. All 26 test completed
>> without error.
>>
>> But when i try to run "gmx or gmx help"
>>
>> There is error no command gmx found. I need your guidance.
>>
>> Best Regards
>>
>> --
>> *Md Imrul Reza Shishir*
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
>> mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] sugar puckering

2016-04-21 Thread Téletchéa Stéphane


Le 21/04/2016 04:24, bharat gupta a écrit :

Dear Gmx Users,

I am interested in calculating cremer-pople parameters for a trisachharide
ligand from its simulation docked with a protein. I found one tool
g_puckering for calculating the parameters but it was written for Gromacs
version 4.0.x and I am using version 5.0.4. I am not able to compile this
tool for my current version of gromacs. So can anybody tell me how can I
calculate such parameters in gromacs ??



1 - contact the authors
2 - adjust the code (I'm interested if you do it ...)
3 - compile it using the version it was meant for, if it parses xtc 
files it should not matter a lot ...


Best,

Stéphane

--
Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design 
In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes 
cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org

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Re: [gmx-users] empty index group

2016-04-21 Thread Justin Lemkul




On 4/21/16 7:29 AM, David Newman wrote:

Hi,

So on Gromacs 4.6.5, I'm using the make_ndx command to try to create a custom
index of a binding pocket on my protein of interest, I want to group 5
non-contiguous residues, I can index them separately and tried to group them
with & but that creates an empty group error because I guess it is for
linking separate options together not separate instances of the same option.
Is there a way to achieve what I'm after?



Your problem is that you used &.  Atoms cannot be in one residue and 
simultaneously in another.  You need the "or" operator, |, e.g.:


r 10 | r 20 | r 30 | r 40 | r 50

because atoms can be in residue 10 OR residue 20 OR ...

-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] empty index group

2016-04-21 Thread David Newman

Hi,

So on Gromacs 4.6.5, I'm using the make_ndx command to try to create a custom 
index of a binding pocket on my protein of interest, I want to group 5 
non-contiguous residues, I can index them separately and tried to group them 
with & but that creates an empty group error because I guess it is for linking 
separate options together not separate instances of the same option. Is there a 
way to achieve what I'm after?

Thanks,

David
-- 
Gromacs Users mailing list

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Re: [gmx-users] problem regarding cut-off and the PME grid spacing

2016-04-21 Thread Justin Lemkul




On 4/21/16 6:57 AM, Tuhin Samanta wrote:

please check it...

[ moleculetype ]
; molname   nrexcl
HOD 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
  1  opls_116   1HOD OW  1  -0.8476
  2  opls_117   1HOD HW  1   0.4238
  3  opls_805   1HOD DW  1   0.4238

#ifndef FLEXIBLE
; [ settles ]
; OWfunct   doh dhh
  ; 10.101   0.16500

;[ exclusions ]
;1  2   3
;2  1   3
;3  1   2
#else
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.1 345000  0.1 345000
1   3   1   0.102   266292  0.102   266292

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   105.7   583 105.7   583



Of course this crashes - you're trying to use a 2-fs time step without any 
constraints.  Reduce dt or treat the water model as rigid.


-Justin


Thanks,
Tuhin

On Thu, Apr 21, 2016 at 3:20 PM, Justin Lemkul  wrote:




On 4/21/16 3:32 AM, Tuhin Samanta wrote:


The topology file for my system - HOD System like that ---



#include "oplsaa.ff/forcefield.itp"

; Include hod topology
#include "hod.itp"

[ system ]
;Name
HOD

[ molecules ]
; Compound#mols
HOD102

.mdp file is like that -

(FOR Energy minimization)

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 0.1   ; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 20; Maximum number of (minimization) steps
to
perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list
and
long range forces
ns_type = grid  ; Method to determine neighbor list
(simple, grid)
rlist   = 1.0   ; Cut-off for making neighbor list (short
range forces)
coulombtype = PME   ; Treatment of long range electrostatic
interactions
rcoulomb= 1.0   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)
constraints = none

For Equilibritaion (NVT)

title   =  NVT equilibration of W10 RM
cpp = /lib/cpp
include = -I../top
integrator  = md; leap-frog integrator
nsteps  = 50   ; 2 * 1 = 20 ns
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100  ; save coordinates every 0.1 ns
nstvout = 100  ; save velocities every 0.1 ns
nstenergy   = 100 ; save energies every 0.1 ns
nstlog  = 100  ; update log file every 0.1 ns
; Bond parameters
continuation= yes   ; continuation from previous run
constraint_algorithm = lincs; holonomic constraints
constraints = none ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 10 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
optimize_fft= yes
; Temperature coupling is on
tcoupl  = Berendsen ; modified Berendsen thermostat
tc-grps = System; two coupling groups - more accurate
tau_t   = 1.0   ; time constant, in ps
ref_t   = 300   ; reference temperature, one for each
group
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell
distribution


Please take a look . I am getting the error like that -- 4 particles
communicated to PME node 4 are more than 2/3 times the cut-off out of the
domain decomposition cell of their charge group in dimension x. This
usually means that your system is not well equilibrated.

If you want I can send you my .itp file also.



Yes, that's actually rather important; the .top itself just #includes

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

2016-04-21 Thread Tuhin Samanta

please check it...

[ moleculetype ]
; molname   nrexcl
HOD 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
 1  opls_116   1HOD OW  1  -0.8476
 2  opls_117   1HOD HW  1   0.4238
 3  opls_805   1HOD DW  1   0.4238

#ifndef FLEXIBLE
; [ settles ]
; OWfunct   doh dhh
 ; 10.101   0.16500

;[ exclusions ]
;1  2   3
;2  1   3
;3  1   2
#else
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.1 345000  0.1 345000
1   3   1   0.102   266292  0.102   266292

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   105.7   583 105.7   583

Thanks,
Tuhin

On Thu, Apr 21, 2016 at 3:20 PM, Justin Lemkul  wrote:

>
>
> On 4/21/16 3:32 AM, Tuhin Samanta wrote:
>
>> The topology file for my system - HOD System like that ---
>>
>>
>>
>> #include "oplsaa.ff/forcefield.itp"
>>
>> ; Include hod topology
>> #include "hod.itp"
>>
>> [ system ]
>> ;Name
>> HOD
>>
>> [ molecules ]
>> ; Compound#mols
>> HOD102
>>
>> .mdp file is like that -
>>
>> (FOR Energy minimization)
>>
>> ; minim.mdp - used as input into grompp to generate em.tpr
>> ; Parameters describing what to do, when to stop and what to save
>> integrator  = steep ; Algorithm (steep = steepest descent
>> minimization)
>> emtol   = 0.1   ; Stop minimization when the maximum force
>> < 1000.0 kJ/mol/nm
>> emstep  = 0.01  ; Energy step size
>> nsteps  = 20; Maximum number of (minimization) steps
>> to
>> perform
>>
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> nstlist = 1 ; Frequency to update the neighbor list
>> and
>> long range forces
>> ns_type = grid  ; Method to determine neighbor list
>> (simple, grid)
>> rlist   = 1.0   ; Cut-off for making neighbor list (short
>> range forces)
>> coulombtype = PME   ; Treatment of long range electrostatic
>> interactions
>> rcoulomb= 1.0   ; Short-range electrostatic cut-off
>> rvdw= 1.0   ; Short-range Van der Waals cut-off
>> pbc = xyz   ; Periodic Boundary Conditions (yes/no)
>> constraints = none
>>
>> For Equilibritaion (NVT)
>>
>> title   =  NVT equilibration of W10 RM
>> cpp = /lib/cpp
>> include = -I../top
>> integrator  = md; leap-frog integrator
>> nsteps  = 50   ; 2 * 1 = 20 ns
>> dt  = 0.002 ; 2 fs
>> ; Output control
>> nstxout = 100  ; save coordinates every 0.1 ns
>> nstvout = 100  ; save velocities every 0.1 ns
>> nstenergy   = 100 ; save energies every 0.1 ns
>> nstlog  = 100  ; update log file every 0.1 ns
>> ; Bond parameters
>> continuation= yes   ; continuation from previous run
>> constraint_algorithm = lincs; holonomic constraints
>> constraints = none ; all bonds (even heavy atom-H bonds)
>> constrained
>> lincs_iter  = 1 ; accuracy of LINCS
>> lincs_order = 4 ; also related to accuracy
>> ; Neighborsearching
>> ns_type = grid  ; search neighboring grid cells
>> nstlist = 10 ; 10 fs
>> rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
>> rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
>> rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
>> ; Electrostatics
>> coulombtype = PME   ; Particle Mesh Ewald for long-range
>> electrostatics
>> pme_order   = 4 ; cubic interpolation
>> fourierspacing  = 0.16  ; grid spacing for FFT
>> optimize_fft= yes
>> ; Temperature coupling is on
>> tcoupl  = Berendsen ; modified Berendsen thermostat
>> tc-grps = System; two coupling groups - more accurate
>> tau_t   = 1.0   ; time constant, in ps
>> ref_t   = 300   ; reference temperature, one for each
>> group
>> ; Pressure coupling is off
>> pcoupl  = no; no pressure coupling in NVT
>> ; Periodic boundary conditions
>> pbc = xyz   ; 3-D PBC
>> ; Dispersion correction
>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = yes   ; assign velocities from Maxwell
>> distribution
>>
>>
>> Please take a look . I am getting the error like that -- 4 particles
>> communicated to PME node 4 are more than 2/3 times the cut-off out of the
>> domain decomposition cell of their charge group in dimension x. This
>> usually means that your system is not well equilibrated.
>>
>> If you want I can

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 119

2016-04-21 Thread Groenhof, Gerrit

Hi,

Indeed, Link atoms have to be added to the .gro file. The atom indexing in the 
.gro file is not used, so no need to renumber. A simple editconf can do that 
for you if too, if you would like to have the numbering correct.  However, you 
need to adjust the total number of atoms at the top of the .gro file. 

for the bonded interactions, you should remove the gb_x , because these defines 
contain the bond type information as well. Easiest is to add a ';' like this 

1851  1853 2   ; gb_10

which means that what comes after is ignored.

good luck,

Gerrit

Message: 3
Date: Thu, 21 Apr 2016 17:43:47 +0900
From: bharat gupta 
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Defining LA atoms in .gro file
Message-ID:

Content-Type: text/plain; charset=UTF-8

Dear GMX Users,

I am trying to perform QM/MM simulation for my system and I need to define
LA for the boundary between QM and MM region. I have the boundary regions
but I don't know how to add them in the gro file. Do I have to manually
modify the .gro file, if that's the case, adding, them manually how do I
renumber the rest of the atoms and residues? Here's what I have done:

 3715YWR   H21 3562   4.283   4.647   4.755 -1.1354  1.0843 -0.8713
  372XXX LA 3563   2.475   3.856   2.040 -0.0020 -0.1066  0.1995
  373XXX LA 3564   0.475   3.856   2.040 -0.0020 -0.1066  0.1995
  374XXX LA 3565   1.475   3.856   2.040 -0.0020 -0.1066  0.1995
  375XXX LA 3566   3.475   3.856   2.040 -0.0020 -0.1066  0.1995
  376XXX LA 3567   0.875   3.856   2.040 -0.0020 -0.1066  0.1995
  377XXX LA 3568   1.575   3.856   2.040 -0.0020 -0.1066  0.1995
  372SOL OW 3563   3.414   3.445   2.243 -0.1786 -0.5561  0.4692
  372SOLHW1 3564   3.479   3.440   2.167  0.5613 -1.1084  1.1215
  372SOLHW2 3565   3.329   3.488   2.212  0.4389  0.0440 -0.4374
  373SOL OW 3566   1.589   3.334   2.348  0.6300  0.1793 -0.1279
  373SOLHW1 3567   1.639   3.413   2.384  1.2205  0.0166 -0.5746
  373SOLHW2 3568   1.588   3.337   2.248 -1.5585  0.9770 -0.1508
  374SOL OW 3569   5.280   6.227   4.070  0.5862 -0.1571 -0.6930

So, I added the LA atoms between atom no H21/3562 and OW/3563 manually.
Please let me whether this is the correct way of adding the LA atoms ?

Also, I need to modify the bond_types as well in the topology file to 5. Is
this the correct way:

1851  1853 2gb_10
 1853  1854 5gb_2
 1853  1855 5gb_21
 1855  1856 5gb_27
 1855  1862 5gb_27
 1856  1857 5gb_27
 1857  1858 5gb_27
 1858  1859 5gb_5
 1858  1860 5gb_13
 1860  1861 5gb_1
 1862  1863 5gb_5
 1862  1864 2gb_10
 1864  1865 2gb_2

I haven't changed the values for C0 for the QM atoms but I have changed
their type to 5.

--
*Best Regards*
BM

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Re: [gmx-users] trouble with ca2+ atom and SEP recognition in Gromacs 5.1.1

2016-04-21 Thread Justin Lemkul




On 4/20/16 3:56 PM, Jayant James wrote:

Hi!
All I have been running into some trouble with CA2+ recognition in GMX
5.1.1.
So some back ground..I have a protein that I am trying to simulate that
has three chains.First chain is 161 amino acids long, second one is about
200AA and the third one is about 280 AA long.
They have their terminal residues given with OXT and "ter" is given after
each chain. Also this protein has two phosphorylated serines that are input
as SEP.
Since I am having two SEP molecules I am using the option#
10 GROMOS96 43a1 force field, extended to include phosphorylated residues

Below is the description of the calcium atoms in the input PDB file
---
ATOM   1283  CA  CA2+D 162  10.494  65.413  -1.733  1.00
78.08   C
ATOM   1284  CA  CA2+D 163  14.370  25.685   8.168  1.00
78.08   C
ATOM   1285  CA  CA2+D 164  18.826  35.294   3.395  1.00
78.08   C

INPUT COMMAND
--
  gmx pdb2gmx -f start.pdb -p new -o new -merge all -ignh


Concerns
-
1) I am hit with error messages that tell me the calcium ions are not
recognized (colored red). I'd appreciate a way to solve this.


They're recognized just fine, but apparently they're disrupting a protein chain. 
 A continuous chain has to be continuous with respect to residue type, 
otherwise pdb2gmx warns you that something is amiss.



2) Also the third chain having the SEP amino acids is not being
recognizing!!! Colored blue


You need to add SEP as a Protein entry in residuetypes.dat.


3) The third chain is 192 aa long. But the program tells that it recognizes
only till 22 aa although a few lines this it seems like it recognizes till
the 192nd aa


See point #2.

-Justin


I'd appreciate any suggetions that would help me tide over these errors

Thank you
James





*ERROR MESSAGE*
--
Opening force field file
/share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/aminoacids.r2b
Reading start.pdb...
Read 3572 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.

Merged chains into joint molecule definitions at 2 places.

There are 1 chains and 0 blocks of water and 443 residues with 3572 atoms

   chain  #res #atoms
   1 'D'   443   3572

All occupancies are one
Opening force field file
/share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/atomtypes.atp
Atomtype 48
Reading residue database... (gromos43a1p)
Opening force field file
/share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper
dihedral
Residue 101
Sorting it all out...
Opening force field file
/share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/aminoacids.hdb
Opening force field file
/share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/aminoacids.n.tdb
Opening force field file
/share/apps/gromacs/5.1.1/share/gromacs/top/gromos43a1p.ff/aminoacids.c.tdb

Back Off! I just backed up new.top to ./#new.top.2#
Processing chain 1 'D' (3572 atoms, 443 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
  protonation. 679 donors and 705 acceptors were found.
There are 937 hydrogen bonds
Will use HISE for residue 223
Will use HISE for residue 35
Will use HISE for residue 102
Will use HISE for residue 173
Identified residue MET1 as a starting terminus.
Warning: Residue CA2+162 in chain has different type (Other) from starting
residue MET1 (Protein).
Warning: Residue CA2+163 in chain has different type (Other) from starting
residue MET1 (Protein).
Warning: Residue CA2+164 in chain has different type (Other) from starting
residue MET1 (Protein).
Identified residue GLU161 as a ending terminus.
Identified residue GLN202 as a starting terminus.
Identified residue LYS288 as a ending terminus.
Identified residue MET1 as a starting terminus.
Warning: Residue SEP23 in chain has different type (Other) from starting
residue MET1 (Protein).
Warning: Residue SEP24 in chain has different type (Other) from starting
residue MET1 (Protein).
Warning: Residue ALA25 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue ASN26 in chain has different type (Protein) from starting
residue MET1 (Protein).
Warning: Residue TYR27 in chain has different type (Protein) from starting
residue MET1 (Protein).
Special Atom Distance matrix:
 MET1   MET45   MET47   MET60   MET80   MET81   MET85
  SD7   SD349   SD368   SD470   SD625   SD633   SD665
MET45   SD349   2.333
MET47   SD368   3.175   1.004
MET60   SD470   1.883   0.496   1.457
MET80   SD625   1.769   0.820   1.424   0.683
MET81   SD633   2.065   0.981   1.341   1.050

Re: [gmx-users] Number of urea molecules for 2.1 M solution

2016-04-21 Thread Justin Lemkul




On 4/21/16 3:00 AM, Divya Dube wrote:

Dear all,

How to calculate number of urea molecules required for a box size of 294.68
nm^3 for 2.1 M urea solution



You have a volume, you have a desired concentration, C = n/V.

-Justin

--
==

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

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

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

==
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Re: [gmx-users] problem regarding cut-off and the PME grid spacing

2016-04-21 Thread Justin Lemkul




On 4/21/16 3:32 AM, Tuhin Samanta wrote:

The topology file for my system - HOD System like that ---



#include "oplsaa.ff/forcefield.itp"

; Include hod topology
#include "hod.itp"

[ system ]
;Name
HOD

[ molecules ]
; Compound#mols
HOD102

.mdp file is like that -

(FOR Energy minimization)

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 0.1   ; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 20; Maximum number of (minimization) steps to
perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and
long range forces
ns_type = grid  ; Method to determine neighbor list
(simple, grid)
rlist   = 1.0   ; Cut-off for making neighbor list (short
range forces)
coulombtype = PME   ; Treatment of long range electrostatic
interactions
rcoulomb= 1.0   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)
constraints = none

For Equilibritaion (NVT)

title   =  NVT equilibration of W10 RM
cpp = /lib/cpp
include = -I../top
integrator  = md; leap-frog integrator
nsteps  = 50   ; 2 * 1 = 20 ns
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100  ; save coordinates every 0.1 ns
nstvout = 100  ; save velocities every 0.1 ns
nstenergy   = 100 ; save energies every 0.1 ns
nstlog  = 100  ; update log file every 0.1 ns
; Bond parameters
continuation= yes   ; continuation from previous run
constraint_algorithm = lincs; holonomic constraints
constraints = none ; all bonds (even heavy atom-H bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 10 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
optimize_fft= yes
; Temperature coupling is on
tcoupl  = Berendsen ; modified Berendsen thermostat
tc-grps = System; two coupling groups - more accurate
tau_t   = 1.0   ; time constant, in ps
ref_t   = 300   ; reference temperature, one for each group
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell
distribution


Please take a look . I am getting the error like that -- 4 particles
communicated to PME node 4 are more than 2/3 times the cut-off out of the
domain decomposition cell of their charge group in dimension x. This
usually means that your system is not well equilibrated.

If you want I can send you my .itp file also.



Yes, that's actually rather important; the .top itself just #includes the .itp 
and therefore contains no useful information.


-Justin


Tuhin


On Wed, Apr 20, 2016 at 10:52 PM, Justin Lemkul  wrote:




On 4/20/16 1:20 PM, Tuhin Samanta wrote:


I have done the energy minimization many times by taking previously
minimized structure.



A box of water should be basically impossible to break.  Either your .mdp
or topology has problems.  Since you've provided neither, there's not much
anyone can do to help you.  The diagnostic walkthrough that Mark linked is
the best source of figuring it out.  Short of that, provide us with your
input topology and .mdp (copied and pasted if small enough for an email, or
linked to a file-sharing service otherwise).

-Justin





On Wed, Apr 20, 2016 at 10:39 PM, Mark Abraham 
wrote:

Hi,


On Wed, 20 Apr 2016 19:04 Tuhin Samanta 
wrote:

Thank Mark for your suggestion.


I was trying to resolve the problem 
" 4 particles communicated to PME node 4 are more than 2/3 times the
cut-off out of the

Re: [gmx-users] NA or SOD in CHARMM36

2016-04-21 Thread Justin Lemkul

On 4/21/16 4:56 AM, Jason Loo Siau Ee wrote:

Hi all,

I'm trying to simulate a protein-ligand complex in POPC membrane using the CHARMM36 forcefield,
which I got from the Mackerell site and included in /share/gromacs/top/. Now when I run grompp I
get the error "Fatal error: No such moleculetype SOD" despite the fact that I have
#include "charmm36.ff/ions.itp" in my topology. A quick check on the ions.itp in
charmm36.ff/ shows the following:

[ moleculetype ]
; molname nrexcl
NA 1

[ atoms ]
; idat type res nr residu name at name cg nr charge
1 SOD 1 NA NA 1 1

Now as I understand sodium is called SOD in CHARMM, so shouldn't all the NA be
SOD instead? As this is from the Mackerell site I'm going to assume there isn't
an error here, so am I about the do something silly? Is there a reason for this
discrepancy (like because genion only adds NA and not SOD)? I've noticed
similar issues with other ions and the water models (SOL instead of TI3P). I'm
guessing I should create a local copy of the modified itp files then?

You should use NA; this is done to follow the GROMACS genion convention that
ions are added by their all-caps elemental symbol. So your -pname in genion
should be NA, which means NA is written to the topology file. SOD is just the
atom type, which is only used by grompp when parsing the actual parameters.

You shouldn't need to make any changes to the files.

-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] NA or SOD in CHARMM36

2016-04-21 Thread Jason Loo Siau Ee

Hi all,

I'm trying to simulate a protein-ligand complex in POPC membrane using the 
CHARMM36 forcefield, which I got from the Mackerell site and included in 
/share/gromacs/top/. Now when I run grompp I get the error "Fatal error: No 
such moleculetype SOD" despite the fact that I have #include 
"charmm36.ff/ions.itp" in my topology. A quick check on the ions.itp in 
charmm36.ff/ shows the following:

[ moleculetype ]
; molname   nrexcl
NA  1

[ atoms ]
; idat type res nr  residu name at name  cg nr  charge
1   SOD 1   NA  NA   1  1

Now as I understand sodium is called SOD in CHARMM, so shouldn't all the NA be 
SOD instead? As this is from the Mackerell site I'm going to assume there isn't 
an error here, so am I about the do something silly? Is there a reason for this 
discrepancy (like because genion only adds NA and not SOD)? I've noticed 
similar issues with other ions and the water models (SOL instead of TI3P). I'm 
guessing I should create a local copy of the modified itp files then?

Regards,
Jason Loo








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Re: [gmx-users] Moving this mailing list to Discourse format

2016-04-21 Thread Mark Abraham

Hi Hannes,

Yes, previous discussion has identified this as a likely key feature, and
thanks for adding confirmation of that. Discourse can be integrated with
functionality for replying to threads from email to suit people who want
that kind of small change to their workflows; that will indeed suit simple
discussions. Obviously there's configurable email activity digests and
notifications also, which provide links to the forum proper.

Mark

On Thu, Apr 21, 2016 at 9:52 AM Hannes Loeffler 
wrote:

> On Thu, 21 Apr 2016 07:11:42 +
> Mark Abraham  wrote:
>
> > Hi people,
> >
> > As part of the new BioExcel project (http://bioexcel.eu/) that
> > supports biomolecular research with codes including GROMACS, we're
> > exploring migrating the gmx-users mailing list to the Discourse
> > format. You can see an example at http://try.discourse.org! This has
> > a number of immediate advantages, including attachments, single-click
> > sign-up, tagging, voting and contributing to old discussions. We
> > might also integrate features like replying to threads via email, or
> > real-time chat. We also know such a change might be something people
> > don't like, and we would like to get a feel for that. The community
> > should like its forum, after all! :-) So please let us know how you
> > feel at http://goo.gl/forms/k8lhTliffO.
>
> I think such a discussion would need a bit more space than just a few
> pre-canned questions.
>
> I am on various mailing lists and happy with my email client as a
> central "collector" of all those discussions.  I am personally not fond
> of another web page interface with its very own features, bells and
> whistles and what not, but typically unlike any other existing one.
> And this is in essence the major shortcoming unless it would be still
> possible to receive all messages through a mailing list as it is now.
>
> Cheers,
> Hannes.
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Re: [gmx-users] Defining LA atoms in .gro file

2016-04-21 Thread bharat gupta

Dear GMX Users,

I am trying to perform QM/MM simulation for my system and I need to define
LA for the boundary between QM and MM region. I have the boundary regions
but I don't know how to add them in the gro file. Do I have to manually
modify the .gro file, if that's the case, adding, them manually how do I
renumber the rest of the atoms and residues? Here's what I have done:

 3715YWR   H21 3562   4.283   4.647   4.755 -1.1354  1.0843 -0.8713
  372XXX LA 3563   2.475   3.856   2.040 -0.0020 -0.1066  0.1995
  373XXX LA 3564   0.475   3.856   2.040 -0.0020 -0.1066  0.1995
  374XXX LA 3565   1.475   3.856   2.040 -0.0020 -0.1066  0.1995
  375XXX LA 3566   3.475   3.856   2.040 -0.0020 -0.1066  0.1995
  376XXX LA 3567   0.875   3.856   2.040 -0.0020 -0.1066  0.1995
  377XXX LA 3568   1.575   3.856   2.040 -0.0020 -0.1066  0.1995
  372SOL OW 3563   3.414   3.445   2.243 -0.1786 -0.5561  0.4692
  372SOLHW1 3564   3.479   3.440   2.167  0.5613 -1.1084  1.1215
  372SOLHW2 3565   3.329   3.488   2.212  0.4389  0.0440 -0.4374
  373SOL OW 3566   1.589   3.334   2.348  0.6300  0.1793 -0.1279
  373SOLHW1 3567   1.639   3.413   2.384  1.2205  0.0166 -0.5746
  373SOLHW2 3568   1.588   3.337   2.248 -1.5585  0.9770 -0.1508
  374SOL OW 3569   5.280   6.227   4.070  0.5862 -0.1571 -0.6930

So, I added the LA atoms between atom no H21/3562 and OW/3563 manually.
Please let me whether this is the correct way of adding the LA atoms ?

Also, I need to modify the bond_types as well in the topology file to 5. Is
this the correct way:

1851  1853 2gb_10
 1853  1854 5gb_2
 1853  1855 5gb_21
 1855  1856 5gb_27
 1855  1862 5gb_27
 1856  1857 5gb_27
 1857  1858 5gb_27
 1858  1859 5gb_5
 1858  1860 5gb_13
 1860  1861 5gb_1
 1862  1863 5gb_5
 1862  1864 2gb_10
 1864  1865 2gb_2

I haven't changed the values for C0 for the QM atoms but I have changed
their type to 5.

-- 
*Best Regards*
BM
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Re: [gmx-users] Moving this mailing list to Discourse format

2016-04-21 Thread Hannes Loeffler

On Thu, 21 Apr 2016 07:11:42 +
Mark Abraham  wrote:

> Hi people,
> 
> As part of the new BioExcel project (http://bioexcel.eu/) that
> supports biomolecular research with codes including GROMACS, we're
> exploring migrating the gmx-users mailing list to the Discourse
> format. You can see an example at http://try.discourse.org! This has
> a number of immediate advantages, including attachments, single-click
> sign-up, tagging, voting and contributing to old discussions. We
> might also integrate features like replying to threads via email, or
> real-time chat. We also know such a change might be something people
> don't like, and we would like to get a feel for that. The community
> should like its forum, after all! :-) So please let us know how you
> feel at http://goo.gl/forms/k8lhTliffO.

I think such a discussion would need a bit more space than just a few
pre-canned questions.

I am on various mailing lists and happy with my email client as a
central "collector" of all those discussions.  I am personally not fond
of another web page interface with its very own features, bells and
whistles and what not, but typically unlike any other existing one.
And this is in essence the major shortcoming unless it would be still
possible to receive all messages through a mailing list as it is now.

Cheers,
Hannes.
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Re: [gmx-users] problem regarding cut-off and the PME grid spacing

2016-04-21 Thread Tuhin Samanta

The topology file for my system - HOD System like that ---



#include "oplsaa.ff/forcefield.itp"

; Include hod topology
#include "hod.itp"

[ system ]
;Name
HOD

[ molecules ]
; Compound#mols
HOD102

.mdp file is like that -

(FOR Energy minimization)

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 0.1   ; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 20; Maximum number of (minimization) steps to
perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and
long range forces
ns_type = grid  ; Method to determine neighbor list
(simple, grid)
rlist   = 1.0   ; Cut-off for making neighbor list (short
range forces)
coulombtype = PME   ; Treatment of long range electrostatic
interactions
rcoulomb= 1.0   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)
constraints = none

For Equilibritaion (NVT)

title   =  NVT equilibration of W10 RM
cpp = /lib/cpp
include = -I../top
integrator  = md; leap-frog integrator
nsteps  = 50   ; 2 * 1 = 20 ns
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100  ; save coordinates every 0.1 ns
nstvout = 100  ; save velocities every 0.1 ns
nstenergy   = 100 ; save energies every 0.1 ns
nstlog  = 100  ; update log file every 0.1 ns
; Bond parameters
continuation= yes   ; continuation from previous run
constraint_algorithm = lincs; holonomic constraints
constraints = none ; all bonds (even heavy atom-H bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 10 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
optimize_fft= yes
; Temperature coupling is on
tcoupl  = Berendsen ; modified Berendsen thermostat
tc-grps = System; two coupling groups - more accurate
tau_t   = 1.0   ; time constant, in ps
ref_t   = 300   ; reference temperature, one for each group
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell
distribution


Please take a look . I am getting the error like that -- 4 particles
communicated to PME node 4 are more than 2/3 times the cut-off out of the
domain decomposition cell of their charge group in dimension x. This
usually means that your system is not well equilibrated.

If you want I can send you my .itp file also.

Tuhin


On Wed, Apr 20, 2016 at 10:52 PM, Justin Lemkul  wrote:

>
>
> On 4/20/16 1:20 PM, Tuhin Samanta wrote:
>
>> I have done the energy minimization many times by taking previously
>> minimized structure.
>>
>>
> A box of water should be basically impossible to break.  Either your .mdp
> or topology has problems.  Since you've provided neither, there's not much
> anyone can do to help you.  The diagnostic walkthrough that Mark linked is
> the best source of figuring it out.  Short of that, provide us with your
> input topology and .mdp (copied and pasted if small enough for an email, or
> linked to a file-sharing service otherwise).
>
> -Justin
>
>
>
>>
>> On Wed, Apr 20, 2016 at 10:39 PM, Mark Abraham 
>> wrote:
>>
>> Hi,
>>>
>>> On Wed, 20 Apr 2016 19:04 Tuhin Samanta 
>>> wrote:
>>>
>>> Thank Mark for your suggestion.

 I was trying to resolve the problem 
 " 4 particles communicated to PME node 4 are more than 2/3 times the
 cut-off out of the domain decomposition cell of their charge group in
 dimension x.
 This usually means that your system

[gmx-users] Moving this mailing list to Discourse format

2016-04-21 Thread Mark Abraham

Hi people,

As part of the new BioExcel project (http://bioexcel.eu/) that supports
biomolecular research with codes including GROMACS, we're exploring
migrating the gmx-users mailing list to the Discourse format. You can see
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and contributing to old discussions. We might also integrate features like
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Cheers,

Mark
GROMACS development manager
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[gmx-users] Number of urea molecules for 2.1 M solution

2016-04-21 Thread Divya Dube

Dear all,

How to calculate number of urea molecules required for a box size of 294.68
nm^3 for 2.1 M urea solution



regds

Divya
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Re: [gmx-users] Installation Problem... No command 'gmx' found

2016-04-21 Thread Email Gmail Pribadi

Hi,

Try gmx [command] . Ex. gmx mdrun -option

Regards,


Husen

> On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote:
> 
> Hi, 
> 
> Try gmx_mpi.
> 
> Regards
> Terry
> 
> 
>> On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir 
>>  wrote:
>> 
>> Dear all user
>> 
>> I install gromacs in my laptop its perfectly ok. But i have problem to
>> install in my desktop there i face problem.
>> In my desktop i want to compile with cuda accelerator and MPI option. I
>> install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all
>> this driver is ok.
>> 
>> For gromacs i run this installation command.
>> 
>> tar -xzvf gromacs-5.1.2.tar.gz
>> cd gromacs-5.1.2.tar.gz
>> mkdir build
>> cd build
>> CMAKE  -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on
>> -DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on
>> make -j16
>> make check
>> sudo make install -j16
>> 
>> source /usr/local/gromacs/bin/GMXRC
>> 
>> In the installation procedure i dont find any error. All 26 test completed
>> without error.
>> 
>> But when i try to run "gmx or gmx help"
>> 
>> There is error no command gmx found. I need your guidance.
>> 
>> Best Regards
>> 
>> -- 
>> *Md Imrul Reza Shishir*
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