[gmx-users] WARNING: Duplicate line found in or between hackblock and rtp entries

[Anurag Dobhal]

Dear Gromacs Users,
I Simulated a Nucleotide pair using OPLS AA force field. while running "
gmx pdb2gmx" I am getting the following warning.

WARNING: Duplicate line found in or between hackblock and rtp entries

How to address this warning ?

Thank You


*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*

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Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

[Billy Williams-Noonan]

Thanks for your reply, I think this is helping.

   Using your equation above I would need about 82TB for 1000 frames...   I
somehow feel that this would be inaccessible for any calculation using just
one node, which is a requirement for g_covar.
I could reduce the frames but I think I would wind up sub-sampling my
system.

   I am selecting the entire system twice in gmx covar to get the entropy
of the system in gmx anaeig (as shown in the command on the original
post).  Are you saying I should just select the protein, ligand and complex
for each ensemble?

Billy



On 21 June 2016 at 16:39, David van der Spoel  wrote:

> On 21/06/16 08:11, Billy Williams-Noonan wrote:
>
>>Sorry, the original post provides an example of the -dt flag with 100ps
>> intervals.
>>
> You can calculate how much space you need by number of atoms (N * 3)^2
> times number of frames times 4 bytes.
>
> Do you select just your biomolecule?
>
>
>> On 21 June 2016 at 16:10, Billy Williams-Noonan <
>> billy.williams-noo...@monash.edu> wrote:
>>
>> Thank you for your reply. :)
>>>
>>>My main problem is with gmx covar which does not have a -skip flag.
>>> As
>>> you can see from the OP I have tried the -dt flag with 250ps intervals.
>>> It
>>> still crashes due to insufficient memory.  It also crasses with 5000ps
>>> intervals, giving me just 20ps of frames to work with for the whole
>>> ensemble.
>>>
>>> Billy
>>>
>>> On 21 June 2016 at 16:00, David van der Spoel 
>>> wrote:
>>>
>>> On 21/06/16 07:34, Billy Williams-Noonan wrote:

 Hi Gromacs Users,
>
>I am running g_mmpbsa.py to calculate the binding enthalpy of a
> cyclic
> peptide in a drug target.  At the same time I am trying to generate
> ensemble estimates for entropy for the protein, ligand and complex.  By
> using these two variables I aim to get an idea of the Gibbs free energy
> of
> binding.
>
>My system for the complex and the protein is some 50,000 atoms
> large,
> with just over 3000 atoms belonging to the proteins, and the rest of
> the
> system is water and ions, to make up a physiological concentration of
> NaCl.  These are approximate estimates and not exact numbers.  gmx
> covar
> seems to keep crashing every time I try to use it to generate
> eigenvectors
> for the system.  These are the commands I am using:
>
>
> "  gmx covar -f md.xtc -s md.tpr -v md.eigenvec.trr -av average.pdb
> -ascii
> covar -xpm covar -xpma covara -l covar -o md.eigenval.xvg -dt 100 -pbc
> yes
> << EOF
> 0
> 0
> EOF  "
>
> and:
>
> "  gmx anaeig -v md.eigenvec.trr -f md.xtc -s md.tpr -entropy -temp
> 300 >
> out.entropy.schlitter  "
>
>
>I have tried this on a local machine with 16GB of RAM and on a
> cluster
> using one core and a node's worth of RAM (128GB).  I do not have access
> to
> more RAM than this.  Any ideas on how I can stop my calculation from
> crashing due to insufficient memory?
>
> Use the -skip or -dt flags.


Kind regards,
>
>Billy
>
>
>
 --
 David van der Spoel, Ph.D., Professor of Biology
 Dept. of Cell & Molec. Biol., Uppsala University.
 Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
 sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
 --
 Gromacs Users mailing list

 * Please search the archive at
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>>>
>>>
>>> --
>>> Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
>>>
>>> *LinkedIn Profile
>>> <
>>> http://www.linkedin.com/profile/preview?locale=en_US&trk=prof-0-sb-preview-primary-button
>>> >
>>> **|*   +61420 382 557
>>>
>>> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
>>> Royal Parade, Parkville, 3052
>>>
>>>
>>>
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Insti

Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

[David van der Spoel]

On 21/06/16 08:11, Billy Williams-Noonan wrote:

   Sorry, the original post provides an example of the -dt flag with 100ps
intervals.
You can calculate how much space you need by number of atoms (N * 3)^2 
times number of frames times 4 bytes.


Do you select just your biomolecule?



On 21 June 2016 at 16:10, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:


Thank you for your reply. :)

   My main problem is with gmx covar which does not have a -skip flag.  As
you can see from the OP I have tried the -dt flag with 250ps intervals.  It
still crashes due to insufficient memory.  It also crasses with 5000ps
intervals, giving me just 20ps of frames to work with for the whole
ensemble.

Billy

On 21 June 2016 at 16:00, David van der Spoel 
wrote:


On 21/06/16 07:34, Billy Williams-Noonan wrote:


Hi Gromacs Users,

   I am running g_mmpbsa.py to calculate the binding enthalpy of a cyclic
peptide in a drug target.  At the same time I am trying to generate
ensemble estimates for entropy for the protein, ligand and complex.  By
using these two variables I aim to get an idea of the Gibbs free energy
of
binding.

   My system for the complex and the protein is some 50,000 atoms large,
with just over 3000 atoms belonging to the proteins, and the rest of the
system is water and ions, to make up a physiological concentration of
NaCl.  These are approximate estimates and not exact numbers.  gmx covar
seems to keep crashing every time I try to use it to generate
eigenvectors
for the system.  These are the commands I am using:


"  gmx covar -f md.xtc -s md.tpr -v md.eigenvec.trr -av average.pdb
-ascii
covar -xpm covar -xpma covara -l covar -o md.eigenval.xvg -dt 100 -pbc
yes
<< EOF
0
0
EOF  "

and:

"  gmx anaeig -v md.eigenvec.trr -f md.xtc -s md.tpr -entropy -temp 300 >
out.entropy.schlitter  "


   I have tried this on a local machine with 16GB of RAM and on a cluster
using one core and a node's worth of RAM (128GB).  I do not have access
to
more RAM than this.  Any ideas on how I can stop my calculation from
crashing due to insufficient memory?


Use the -skip or -dt flags.



   Kind regards,

   Billy




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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--
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052








--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

[Billy Williams-Noonan]

   Sorry, the original post provides an example of the -dt flag with 100ps
intervals.

On 21 June 2016 at 16:10, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:

> Thank you for your reply. :)
>
>My main problem is with gmx covar which does not have a -skip flag.  As
> you can see from the OP I have tried the -dt flag with 250ps intervals.  It
> still crashes due to insufficient memory.  It also crasses with 5000ps
> intervals, giving me just 20ps of frames to work with for the whole
> ensemble.
>
> Billy
>
> On 21 June 2016 at 16:00, David van der Spoel 
> wrote:
>
>> On 21/06/16 07:34, Billy Williams-Noonan wrote:
>>
>>> Hi Gromacs Users,
>>>
>>>I am running g_mmpbsa.py to calculate the binding enthalpy of a cyclic
>>> peptide in a drug target.  At the same time I am trying to generate
>>> ensemble estimates for entropy for the protein, ligand and complex.  By
>>> using these two variables I aim to get an idea of the Gibbs free energy
>>> of
>>> binding.
>>>
>>>My system for the complex and the protein is some 50,000 atoms large,
>>> with just over 3000 atoms belonging to the proteins, and the rest of the
>>> system is water and ions, to make up a physiological concentration of
>>> NaCl.  These are approximate estimates and not exact numbers.  gmx covar
>>> seems to keep crashing every time I try to use it to generate
>>> eigenvectors
>>> for the system.  These are the commands I am using:
>>>
>>>
>>> "  gmx covar -f md.xtc -s md.tpr -v md.eigenvec.trr -av average.pdb
>>> -ascii
>>> covar -xpm covar -xpma covara -l covar -o md.eigenval.xvg -dt 100 -pbc
>>> yes
>>> << EOF
>>> 0
>>> 0
>>> EOF  "
>>>
>>> and:
>>>
>>> "  gmx anaeig -v md.eigenvec.trr -f md.xtc -s md.tpr -entropy -temp 300 >
>>> out.entropy.schlitter  "
>>>
>>>
>>>I have tried this on a local machine with 16GB of RAM and on a cluster
>>> using one core and a node's worth of RAM (128GB).  I do not have access
>>> to
>>> more RAM than this.  Any ideas on how I can stop my calculation from
>>> crashing due to insufficient memory?
>>>
>> Use the -skip or -dt flags.
>>
>>
>>>Kind regards,
>>>
>>>Billy
>>>
>>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>> --
>> 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.
>>
>
>
>
> --
> Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon
>
> *LinkedIn Profile
> 
> **|*   +61420 382 557
>
> Monash Institute for Pharmaceutical Sciences ( *MIPS* )
> Royal Parade, Parkville, 3052
>
>


-- 
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

[Billy Williams-Noonan]

Thank you for your reply. :)

   My main problem is with gmx covar which does not have a -skip flag.  As
you can see from the OP I have tried the -dt flag with 250ps intervals.  It
still crashes due to insufficient memory.  It also crasses with 5000ps
intervals, giving me just 20ps of frames to work with for the whole
ensemble.

Billy

On 21 June 2016 at 16:00, David van der Spoel  wrote:

> On 21/06/16 07:34, Billy Williams-Noonan wrote:
>
>> Hi Gromacs Users,
>>
>>I am running g_mmpbsa.py to calculate the binding enthalpy of a cyclic
>> peptide in a drug target.  At the same time I am trying to generate
>> ensemble estimates for entropy for the protein, ligand and complex.  By
>> using these two variables I aim to get an idea of the Gibbs free energy of
>> binding.
>>
>>My system for the complex and the protein is some 50,000 atoms large,
>> with just over 3000 atoms belonging to the proteins, and the rest of the
>> system is water and ions, to make up a physiological concentration of
>> NaCl.  These are approximate estimates and not exact numbers.  gmx covar
>> seems to keep crashing every time I try to use it to generate eigenvectors
>> for the system.  These are the commands I am using:
>>
>>
>> "  gmx covar -f md.xtc -s md.tpr -v md.eigenvec.trr -av average.pdb -ascii
>> covar -xpm covar -xpma covara -l covar -o md.eigenval.xvg -dt 100 -pbc yes
>> << EOF
>> 0
>> 0
>> EOF  "
>>
>> and:
>>
>> "  gmx anaeig -v md.eigenvec.trr -f md.xtc -s md.tpr -entropy -temp 300 >
>> out.entropy.schlitter  "
>>
>>
>>I have tried this on a local machine with 16GB of RAM and on a cluster
>> using one core and a node's worth of RAM (128GB).  I do not have access to
>> more RAM than this.  Any ideas on how I can stop my calculation from
>> crashing due to insufficient memory?
>>
> Use the -skip or -dt flags.
>
>
>>Kind regards,
>>
>>Billy
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> 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.
>



-- 
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

[David van der Spoel]

On 21/06/16 07:34, Billy Williams-Noonan wrote:

Hi Gromacs Users,

   I am running g_mmpbsa.py to calculate the binding enthalpy of a cyclic
peptide in a drug target.  At the same time I am trying to generate
ensemble estimates for entropy for the protein, ligand and complex.  By
using these two variables I aim to get an idea of the Gibbs free energy of
binding.

   My system for the complex and the protein is some 50,000 atoms large,
with just over 3000 atoms belonging to the proteins, and the rest of the
system is water and ions, to make up a physiological concentration of
NaCl.  These are approximate estimates and not exact numbers.  gmx covar
seems to keep crashing every time I try to use it to generate eigenvectors
for the system.  These are the commands I am using:


"  gmx covar -f md.xtc -s md.tpr -v md.eigenvec.trr -av average.pdb -ascii
covar -xpm covar -xpma covara -l covar -o md.eigenval.xvg -dt 100 -pbc yes
<< EOF
0
0
EOF  "

and:

"  gmx anaeig -v md.eigenvec.trr -f md.xtc -s md.tpr -entropy -temp 300 >
out.entropy.schlitter  "


   I have tried this on a local machine with 16GB of RAM and on a cluster
using one core and a node's worth of RAM (128GB).  I do not have access to
more RAM than this.  Any ideas on how I can stop my calculation from
crashing due to insufficient memory?

Use the -skip or -dt flags.



   Kind regards,

   Billy




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
Gromacs Users mailing list

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[gmx-users] gmx convert-tpr

[amitbehra]

Hello gmx_users,
I was running a simulation and the wall time got exceeded in the cluster.
I am thinking to use  gmx convert-tpr. -extend (time)
Does this method have any drawbacks. If so what other methods can I try to
resume my simulation.

Regards,


Amit Behera
Research Scholar
Dept. of Chemical Engineering,
IISc
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[gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

[Billy Williams-Noonan]

Hi Gromacs Users,

   I am running g_mmpbsa.py to calculate the binding enthalpy of a cyclic
peptide in a drug target.  At the same time I am trying to generate
ensemble estimates for entropy for the protein, ligand and complex.  By
using these two variables I aim to get an idea of the Gibbs free energy of
binding.

   My system for the complex and the protein is some 50,000 atoms large,
with just over 3000 atoms belonging to the proteins, and the rest of the
system is water and ions, to make up a physiological concentration of
NaCl.  These are approximate estimates and not exact numbers.  gmx covar
seems to keep crashing every time I try to use it to generate eigenvectors
for the system.  These are the commands I am using:


"  gmx covar -f md.xtc -s md.tpr -v md.eigenvec.trr -av average.pdb -ascii
covar -xpm covar -xpma covara -l covar -o md.eigenval.xvg -dt 100 -pbc yes
<< EOF
0
0
EOF  "

and:

"  gmx anaeig -v md.eigenvec.trr -f md.xtc -s md.tpr -entropy -temp 300 >
out.entropy.schlitter  "


   I have tried this on a local machine with 16GB of RAM and on a cluster
using one core and a node's worth of RAM (128GB).  I do not have access to
more RAM than this.  Any ideas on how I can stop my calculation from
crashing due to insufficient memory?

   Kind regards,

   Billy

-- 
Billy Noonan*|*PhD Student*|*Bsci ( *Adv* ), IA Hon

*LinkedIn Profile

**|*   +61420 382 557

Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
-- 
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[gmx-users] Tutorial #3 : Umbrella Sampling (By Justin Lemkul)

[amitbehra]

Hello,
The summary_distances.dat file contains only one column ( the column for
COM is missing).
I am using GROMACS 5.1.2. How to solve this issue.

Regards,
Amit Behera
Research Scholar,
Dept. of Chemical Engineering,
IISc
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Re: [gmx-users] converting the frcmod file and off file to gromacs

[OuyangYanhua]

Thank you for your helpful example.
> 在 2016年6月20日，下午11:17，Marlon Sidore  写道：
> 
> Hi,
> 
> What you want is to convert these from amber (kcal) to gromacs (kJ). I
> followed successfully another post from the mailing list here:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-September/101115.html
> 
> What you should do is make sure your conversion is right, by taking an
> example from the amber forcefield in amber format and its equivalent in
> gromacs format, before applying that conversion on your new parameters.
> 
> Hope that helps.
> 
> Marlon Sidore
> 
> 
> PhD Student
> Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
> CNRS - UMR7255
> 31, Chemin Joseph Aiguier
> 13402 cedex 20 Marseille
> France
> 
> 
> 2016-06-20 16:22 GMT+02:00 Mark Abraham :
> 
>> Hi,
>> 
>> It sounds like what you want to look for is the documentation for those
>> file formats.
>> 
>> Mark
>> 
>> On Sun, 19 Jun 2016 10:05 OuyangYanhua <15901283...@163.com> wrote:
>> 
>>> Hi,
>>> I am simulating a protein phosphorylated on Ser and Thr residues using
>>> AMBER99SB-ILDN ff with Gromacs 5.0. I read the paper that I can use the
>>> phophorylation parameters in the
>>> http://sites.pharmacy.manchester.ac.uk/bryce/amber <
>>> http://sites.pharmacy.manchester.ac.uk/bryce/amber> . However it is
>>> difficult for me to read the parameters and statistics in the frcmod and
>>> off files. So I have trouble in converting the statistics in framod files
>>> and off file to gromacs files, such as .rtp, ffbond.itp.
>>> 
>>> Best regards,
>>> Ouyang
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at
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>>> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] converting the frcmod file and off file to gromacs

[OuyangYanhua]

Thank you for your recommend.
> 在 2016年6月20日，下午10:22，Mark Abraham  写道：
> 
> Hi,
> 
> It sounds like what you want to look for is the documentation for those
> file formats.
> 
> Mark
> 
> On Sun, 19 Jun 2016 10:05 OuyangYanhua <15901283...@163.com> wrote:
> 
>> Hi,
>> I am simulating a protein phosphorylated on Ser and Thr residues using
>> AMBER99SB-ILDN ff with Gromacs 5.0. I read the paper that I can use the
>> phophorylation parameters in the
>> http://sites.pharmacy.manchester.ac.uk/bryce/amber <
>> http://sites.pharmacy.manchester.ac.uk/bryce/amber> . However it is
>> difficult for me to read the parameters and statistics in the frcmod and
>> off files. So I have trouble in converting the statistics in framod files
>> and off file to gromacs files, such as .rtp, ffbond.itp.
>> 
>> Best regards,
>> Ouyang
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
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>> send a mail to gmx-users-requ...@gromacs.org.
>> 
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Re: [gmx-users] Job Output stops being written during long simulations on HPC cluster

[Mark Abraham]

Hi,

First, what GROMACS version is this? If not 5.1.2, then please try that :-)
Otherwise, that's all a bit confusing. Some of the output refers to 16
ranks and others to 9 threads, but you refer to other numbers of cores.
There's no known problem with Intel MPI or compiler, but people run/test
with those relatively less often. You could try other infrastructure, but
frankly it seems more likely that your simulation has instability that you
could probe with more frequent output, or solve with longer/more gentle
equilibration.

Mark

On Tue, Jun 21, 2016 at 1:36 AM Benjamin Joseph Coscia <
benjamin.cos...@colorado.edu> wrote:

> Hi everyone,
>
> I have been attempting to run some long simulations on a supercomputer at
> the University of Colorado at Boulder. I am trying to run simulations for
> about 200 ns. I have done tests using 48 cores and 96 cores. In each case
> output stops being written at the same time step (~50 million steps). This
> is only about half of the simulation time I wanted. According to SLURM, the
> job is still running days past when it stopped outputting.
>
> I checked how much space is being taken up by output files. The largest
> file is the trajectory at ~0.2 GB. I am only outputting data every 1
> million steps. I am convinced that this isn't a memory issue.
>
> I've reached out to the people who run the supercomputer and they are not
> positive what is going on. One of the guys there ran a system trace on the
> 'gmx_mpi mdrun' process and got the following output by looking at one of
> the nodes that is hung up:
>
> [root@node0636 ~]# ps -ef | grep beco
> root 2053 32739 0 20:48 pts/1 00:00:00 grep beco
> beco4952 17561 17557 0 Jun14 ? 00:00:00 /bin/bash
> /tmp/node0636/job1470980/slurm_script
> beco4952 17597 17561 0 Jun14 ? 00:00:00 /bin/bash
> /projects/beco4952/Gromacs/Pores/GitHub/Shell-Scripts/Build_and_Sim.sh -M
> monomer1.pdb -I steep -S 5 -c verlet -t 10 -o 6 -r 3 -p 40 -P 4 -w 10
> -l 20 -x 8.0 -y 8.0 -e 0.1 -T Equilibration in Vacuum -C verlet -i md -D
> 0.002 -L 200 -f 100 -v v-rescale -K 300 -b berendsen -Y semiisotropic -B 1
> -R 4.5e-5 -Z xyz -V 1 -n 8 -s off -m on
> beco4952 18307 17597 0 Jun14 ? 00:00:00 /bin/sh
> /curc/tools/x86_64/rh6/software/impi/5.0.3.048/bin64/mpirun -np 16 gmx_mpi
> mdrun -v -deffnm wiggle
> beco4952 18313 18307 0 Jun14 ? 00:01:34 mpiexec.hydra -np 16 gmx_mpi mdrun
> -v -deffnm wiggle
> beco4952 18314 18313 0 Jun14 ? 00:00:00 /curc/slurm/slurm/current/bin/srun
> --nodelist
> node0636,node0637,node0638,node0639,node0640,node0641,node0642,node0643 -N
> 8 -n 8 /curc/tools/x86_64/rh6/software/impi/5.0.3.048/bin64/pmi_proxy
> --control-port 
> node0636.rc.int.colorado.edu:41464 --pmi-connect lazy-cache
> --pmi-aggregate -s 0 --rmk slurm --launcher slurm --demux poll --pgid 0
> --enable-stdin 1 --retries 10 --control-code 156865336 --usize -2
> --proxy-id -1
> beco4952 18315 18314 0 Jun14 ? 00:00:00 /curc/slurm/slurm/current/bin/srun
> --nodelist
> node0636,node0637,node0638,node0639,node0640,node0641,node0642,node0643 -N
> 8 -n 8 /curc/tools/x86_64/rh6/software/impi/5.0.3.048/bin64/pmi_proxy
> --control-port 
> node0636.rc.int.colorado.edu:41464 --pmi-connect lazy-cache
> --pmi-aggregate -s 0 --rmk slurm --launcher slurm --demux poll --pgid 0
> --enable-stdin 1 --retries 10 --control-code 156865336 --usize -2
> --proxy-id -1
> beco4952 18334 18329 0 Jun14 ? 00:01:00
> /curc/tools/x86_64/rh6/software/impi/5.0.3.048/bin64/pmi_proxy
> --control-port node0636.rc.int.colorado.edu:41464 --pmi-connect lazy-cache
> --pmi-aggregate -s 0 --rmk slurm --launcher slurm --demux poll --pgid 0
> --enable-stdin 1 --retries 10 --control-code 156865336 --usize -2
> --proxy-id -1
> beco4952 18354 18334 99 Jun14 ? 13-20:24:21 gmx_mpi mdrun -v -deffnm wiggle
> beco4952 18355 18334 99 Jun14 ? 13-20:30:41 gmx_mpi mdrun -v -deffnm wiggle
>
> [root@node0636 ~]# strace -f -p 18354
> Process 18354 attached with 9 threads - interrupt to quit
> [pid 18380] futex(0x2b76d6461484, FUTEX_WAIT_PRIVATE, 1, NULL  ...>
> [pid 18378] futex(0x2b76d6462984, FUTEX_WAIT_PRIVATE, 1, NULL  ...>
> [pid 18375] futex(0x2b76d6475484, FUTEX_WAIT_PRIVATE, 3, NULL  ...>
> [pid 18374] futex(0x2b76d6476984, FUTEX_WAIT_PRIVATE, 3, NULL  ...>
> [pid 18368] restart_syscall(<... resuming interrupted call ...>  ...>
> [pid 18377] futex(0x2b76d6463e84, FUTEX_WAIT_PRIVATE, 3, NULL  ...>
> [pid 18364] restart_syscall(<... resuming interrupted call ...>  ...>
> [pid 18354] futex(0x2b76d6477784, FUTEX_WAIT_PRIVATE, 1, NULL  ...>
> [pid 18373] restart_syscall(<... resuming interrupted call ...>) = -1
> ETIMEDOUT (Connection timed out)
> [pid 18373] futex(0x2b76d0736a00, FUTEX_WAKE_PRIVATE, 1) = 0
> [pid 18373] futex(0x2b76d0736a44,
> FUTEX_WAIT_BITSET_PRIVATE|FUTEX_CLOCK_REALTIME, 3631433, {1466303205,
> 353534000}, ) = -1 ETIMEDOUT (Connection timed out)
> [pid 18373] futex(0x2b76d0736a00, FUTEX_WAK

[gmx-users] Job Output stops being written during long simulations on HPC cluster

[Benjamin Joseph Coscia]

Hi everyone,

I have been attempting to run some long simulations on a supercomputer at
the University of Colorado at Boulder. I am trying to run simulations for
about 200 ns. I have done tests using 48 cores and 96 cores. In each case
output stops being written at the same time step (~50 million steps). This
is only about half of the simulation time I wanted. According to SLURM, the
job is still running days past when it stopped outputting.

I checked how much space is being taken up by output files. The largest
file is the trajectory at ~0.2 GB. I am only outputting data every 1
million steps. I am convinced that this isn't a memory issue.

I've reached out to the people who run the supercomputer and they are not
positive what is going on. One of the guys there ran a system trace on the
'gmx_mpi mdrun' process and got the following output by looking at one of
the nodes that is hung up:

[root@node0636 ~]# ps -ef | grep beco
root 2053 32739 0 20:48 pts/1 00:00:00 grep beco
beco4952 17561 17557 0 Jun14 ? 00:00:00 /bin/bash
/tmp/node0636/job1470980/slurm_script
beco4952 17597 17561 0 Jun14 ? 00:00:00 /bin/bash
/projects/beco4952/Gromacs/Pores/GitHub/Shell-Scripts/Build_and_Sim.sh -M
monomer1.pdb -I steep -S 5 -c verlet -t 10 -o 6 -r 3 -p 40 -P 4 -w 10
-l 20 -x 8.0 -y 8.0 -e 0.1 -T Equilibration in Vacuum -C verlet -i md -D
0.002 -L 200 -f 100 -v v-rescale -K 300 -b berendsen -Y semiisotropic -B 1
-R 4.5e-5 -Z xyz -V 1 -n 8 -s off -m on
beco4952 18307 17597 0 Jun14 ? 00:00:00 /bin/sh
/curc/tools/x86_64/rh6/software/impi/5.0.3.048/bin64/mpirun -np 16 gmx_mpi
mdrun -v -deffnm wiggle
beco4952 18313 18307 0 Jun14 ? 00:01:34 mpiexec.hydra -np 16 gmx_mpi mdrun
-v -deffnm wiggle
beco4952 18314 18313 0 Jun14 ? 00:00:00 /curc/slurm/slurm/current/bin/srun
--nodelist
node0636,node0637,node0638,node0639,node0640,node0641,node0642,node0643 -N
8 -n 8 /curc/tools/x86_64/rh6/software/impi/5.0.3.048/bin64/pmi_proxy
--control-port node0636.rc.int.colorado.edu:41464 --pmi-connect lazy-cache
--pmi-aggregate -s 0 --rmk slurm --launcher slurm --demux poll --pgid 0
--enable-stdin 1 --retries 10 --control-code 156865336 --usize -2
--proxy-id -1
beco4952 18315 18314 0 Jun14 ? 00:00:00 /curc/slurm/slurm/current/bin/srun
--nodelist
node0636,node0637,node0638,node0639,node0640,node0641,node0642,node0643 -N
8 -n 8 /curc/tools/x86_64/rh6/software/impi/5.0.3.048/bin64/pmi_proxy
--control-port node0636.rc.int.colorado.edu:41464 --pmi-connect lazy-cache
--pmi-aggregate -s 0 --rmk slurm --launcher slurm --demux poll --pgid 0
--enable-stdin 1 --retries 10 --control-code 156865336 --usize -2
--proxy-id -1
beco4952 18334 18329 0 Jun14 ? 00:01:00
/curc/tools/x86_64/rh6/software/impi/5.0.3.048/bin64/pmi_proxy
--control-port node0636.rc.int.colorado.edu:41464 --pmi-connect lazy-cache
--pmi-aggregate -s 0 --rmk slurm --launcher slurm --demux poll --pgid 0
--enable-stdin 1 --retries 10 --control-code 156865336 --usize -2
--proxy-id -1
beco4952 18354 18334 99 Jun14 ? 13-20:24:21 gmx_mpi mdrun -v -deffnm wiggle
beco4952 18355 18334 99 Jun14 ? 13-20:30:41 gmx_mpi mdrun -v -deffnm wiggle

[root@node0636 ~]# strace -f -p 18354
Process 18354 attached with 9 threads - interrupt to quit
[pid 18380] futex(0x2b76d6461484, FUTEX_WAIT_PRIVATE, 1, NULL 
[pid 18378] futex(0x2b76d6462984, FUTEX_WAIT_PRIVATE, 1, NULL 
[pid 18375] futex(0x2b76d6475484, FUTEX_WAIT_PRIVATE, 3, NULL 
[pid 18374] futex(0x2b76d6476984, FUTEX_WAIT_PRIVATE, 3, NULL 
[pid 18368] restart_syscall(<... resuming interrupted call ...> 
[pid 18377] futex(0x2b76d6463e84, FUTEX_WAIT_PRIVATE, 3, NULL 
[pid 18364] restart_syscall(<... resuming interrupted call ...> 
[pid 18354] futex(0x2b76d6477784, FUTEX_WAIT_PRIVATE, 1, NULL 
[pid 18373] restart_syscall(<... resuming interrupted call ...>) = -1
ETIMEDOUT (Connection timed out)
[pid 18373] futex(0x2b76d0736a00, FUTEX_WAKE_PRIVATE, 1) = 0
[pid 18373] futex(0x2b76d0736a44,
FUTEX_WAIT_BITSET_PRIVATE|FUTEX_CLOCK_REALTIME, 3631433, {1466303205,
353534000}, ) = -1 ETIMEDOUT (Connection timed out)
[pid 18373] futex(0x2b76d0736a00, FUTEX_WAKE_PRIVATE, 1) = 0
[pid 18373] futex(0x2b76d0736a44,
FUTEX_WAIT_BITSET_PRIVATE|FUTEX_CLOCK_REALTIME, 3631435, {1466303205,
553978000}, ) = -1 ETIMEDOUT (Connection timed out)
[pid 18373] futex(0x2b76d0736a00, FUTEX_WAKE_PRIVATE, 1) = 0
[pid 18373] futex(0x2b76d0736a44,
FUTEX_WAIT_BITSET_PRIVATE|FUTEX_CLOCK_REALTIME, 3631437, {1466303205,
754503000}, ) = -1 ETIMEDOUT (Connection timed out)
[pid 18373] futex(0x2b76d0736a00, FUTEX_WAKE_PRIVATE, 1) = 0
[pid 18373] futex(0x2b76d0736a44,
FUTEX_WAIT_BITSET_PRIVATE|FUTEX_CLOCK_REALTIME, 3631439, {1466303205,
954902000}, ) = -1 ETIMEDOUT (Connection timed out)
[pid 18373] futex(0x2b76d0736a00, FUTEX_WAKE_PRIVATE, 1) = 0
[pid 18373] futex(0x2b76d0736a44,
FUTEX_WAIT_BITSET_PRIVATE|FUTEX_CLOCK_REALTIME, 3631441, {1466303206,
155424000}, ) = -1 ETIMEDOUT (Connection timed out)
[pid 18373] futex(0x2b76d0736a00, FUTEX_WAKE_PRIVATE, 1) = 0
[pid

Re: [gmx-users] Tutorial 2: KALP-15 in DPPC

[Justin Lemkul]

On 6/20/16 4:08 PM, Kyle Titus-Glover wrote:

Sure, I can gather up the files and send them in a compressed folder to you
school email if that's ok.



Yes.  The sequence of commands (in an executable script) is also essential.  A 
dump of files is only a small part of the equation.


-Justin



Kyle Titus-Glover


On Mon, Jun 20, 2016 at 3:45 PM, Justin Lemkul  wrote:




On 6/20/16 3:11 PM, Kyle Titus-Glover wrote:


However, I did look into system_shrink1.gro and saw that the file was
missing the peptides and that 2 DPPC molecules still remained undeleted.
Should I manually correct the coordinate file?



No, you should correct whatever it is that you're doing :)  InflateGRO
can't un-delete lipids and it doesn't delete protein.  So you're issuing a
command incorrectly, mismanaging files, or something else.

As this is not actually a GROMACS problem, we can continue this off-list
if needed.  I will need any relevant input and output files and an exact
(copy-paste) of any commands used.  The tutorial works "out of the box," so
there's something being mishandled if it's not.

-Justin


On Mon, Jun 20, 2016 at 3:09 PM, Kyle Titus-Glover  wrote:


I tried restarting the whole process to go back and carefully look and

make sure that nothing was spelled right. Bu I still get the same error.


On Mon, Jun 20, 2016 at 2:36 PM, Justin Lemkul  wrote:




On 6/20/16 2:32 PM, Kyle Titus-Glover wrote:

Hey everyone,


I've been working on the Justin Lemkul's 2nd tutorial and just can't
seem
to get past 2. packing the lipids around the protein and 3. solvating
with
water. The follow the instructions step by step but for some reason as
I
try to run EM  with

gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp

I get hit with this error:

Fatal error:
number of coordinates in coordinate file (system_shrink1.gro, 6400)
 does not match topology (topol.top, 6438)


6400 is the number of atoms in the 128-lipid DPPC bilayer (128 * 50 =

6400) so something has gone badly wrong here.  Your coordinate file at
this
point should have the peptide and 126 lipids; the InflateGRO output
below
looks correct. Check the contents of system_shrink1.gro and make sure
you
haven't perhaps accidentally renamed a file something that it shouldn't
be.

-Justin

I figured that since my number of molecules were off that the problem
was


either the way I updated the molecules section of my topol.top fill by
adding
DPPC   126

after seeing this when adding lipids:

There are 128 lipids...
with 50 atoms per lipid..

Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet

Centering protein
Checking for overlap
...this might actually take a while
100 % done...
There are 2 lipids within cut-off range...
1 will be removed from the upper leaflet...
1 will be removed from the lower leaflet...

But for some reason I can't seem to start the EM iterations because of
this
error.

Sincerely,

Kyle Titus-Glover
Virginia Tech '17 | Engineering Science & Mechanics
Dean's Research Assistant, College of Engineering
443-802-4058


--

==

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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Gromacs Users mailing list

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posting!

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* 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.






--
==

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

==
--
Gromacs Users mailing list

* Please search the archive at
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send a mail to gmx-users-requ...@gromacs.org.



--
==

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.

Re: [gmx-users] Tutorial 2: KALP-15 in DPPC

[Kyle Titus-Glover]

Sure, I can gather up the files and send them in a compressed folder to you
school email if that's ok.


Kyle Titus-Glover


On Mon, Jun 20, 2016 at 3:45 PM, Justin Lemkul  wrote:

>
>
> On 6/20/16 3:11 PM, Kyle Titus-Glover wrote:
>
>> However, I did look into system_shrink1.gro and saw that the file was
>> missing the peptides and that 2 DPPC molecules still remained undeleted.
>> Should I manually correct the coordinate file?
>>
>>
> No, you should correct whatever it is that you're doing :)  InflateGRO
> can't un-delete lipids and it doesn't delete protein.  So you're issuing a
> command incorrectly, mismanaging files, or something else.
>
> As this is not actually a GROMACS problem, we can continue this off-list
> if needed.  I will need any relevant input and output files and an exact
> (copy-paste) of any commands used.  The tutorial works "out of the box," so
> there's something being mishandled if it's not.
>
> -Justin
>
>
> On Mon, Jun 20, 2016 at 3:09 PM, Kyle Titus-Glover  wrote:
>>
>> I tried restarting the whole process to go back and carefully look and
>>> make sure that nothing was spelled right. Bu I still get the same error.
>>>
>>>
>>> On Mon, Jun 20, 2016 at 2:36 PM, Justin Lemkul  wrote:
>>>
>>>

 On 6/20/16 2:32 PM, Kyle Titus-Glover wrote:

 Hey everyone,
>
> I've been working on the Justin Lemkul's 2nd tutorial and just can't
> seem
> to get past 2. packing the lipids around the protein and 3. solvating
> with
> water. The follow the instructions step by step but for some reason as
> I
> try to run EM  with
>
> gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp
>
> I get hit with this error:
>
> Fatal error:
> number of coordinates in coordinate file (system_shrink1.gro, 6400)
>  does not match topology (topol.top, 6438)
>
>
> 6400 is the number of atoms in the 128-lipid DPPC bilayer (128 * 50 =
 6400) so something has gone badly wrong here.  Your coordinate file at
 this
 point should have the peptide and 126 lipids; the InflateGRO output
 below
 looks correct. Check the contents of system_shrink1.gro and make sure
 you
 haven't perhaps accidentally renamed a file something that it shouldn't
 be.

 -Justin

 I figured that since my number of molecules were off that the problem
 was

> either the way I updated the molecules section of my topol.top fill by
> adding
> DPPC   126
>
> after seeing this when adding lipids:
>
> There are 128 lipids...
> with 50 atoms per lipid..
>
> Determining upper and lower leaflet...
> 64 lipids in the upper...
> 64 lipids in the lower leaflet
>
> Centering protein
> Checking for overlap
> ...this might actually take a while
> 100 % done...
> There are 2 lipids within cut-off range...
> 1 will be removed from the upper leaflet...
> 1 will be removed from the lower leaflet...
>
> But for some reason I can't seem to start the EM iterations because of
> this
> error.
>
> Sincerely,
>
> Kyle Titus-Glover
> Virginia Tech '17 | Engineering Science & Mechanics
> Dean's Research Assistant, College of Engineering
> 443-802-4058
>
>
> --
 ==

 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

 ==
 --
 Gromacs Users mailing list

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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
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (

Re: [gmx-users] Gaussian/GROMACS (? ?)

[Groenhof, Gerrit]

To enable QM/MM with Gaussian compile gromacs with 
GMX_QMMM_PROGRAM:STRING=gaussian
If you have compiled already you can change that in you CMakeCache.text for 
example and recompile.

After that you can use the gau script. You need to set $GMX_QM_GAUSS_DIR to the 
location of that script and 

GMX_QM_GAUSS_EXE to the script. Finally, use the group cutoff scheme in 5.1.2. 

Gerrit





I am wondering who happened to have the experience to compile GROMACS with 
Gaussian09 so that Hybrid QM/MM could be achieved. I have read and downloaded 
the 'gau' script, but I am not sure if I would compile GROMACS with QMMM 
firstly. Would anyone give me some guide? I am using GROMACS 5.1.2. Thanks!



Zhuo


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Re: [gmx-users] Tutorial 2: KALP-15 in DPPC

[Justin Lemkul]

On 6/20/16 3:11 PM, Kyle Titus-Glover wrote:

However, I did look into system_shrink1.gro and saw that the file was
missing the peptides and that 2 DPPC molecules still remained undeleted.
Should I manually correct the coordinate file?



No, you should correct whatever it is that you're doing :)  InflateGRO can't 
un-delete lipids and it doesn't delete protein.  So you're issuing a command 
incorrectly, mismanaging files, or something else.


As this is not actually a GROMACS problem, we can continue this off-list if 
needed.  I will need any relevant input and output files and an exact 
(copy-paste) of any commands used.  The tutorial works "out of the box," so 
there's something being mishandled if it's not.


-Justin


On Mon, Jun 20, 2016 at 3:09 PM, Kyle Titus-Glover  wrote:


I tried restarting the whole process to go back and carefully look and
make sure that nothing was spelled right. Bu I still get the same error.


On Mon, Jun 20, 2016 at 2:36 PM, Justin Lemkul  wrote:




On 6/20/16 2:32 PM, Kyle Titus-Glover wrote:


Hey everyone,

I've been working on the Justin Lemkul's 2nd tutorial and just can't seem
to get past 2. packing the lipids around the protein and 3. solvating
with
water. The follow the instructions step by step but for some reason as I
try to run EM  with

gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp

I get hit with this error:

Fatal error:
number of coordinates in coordinate file (system_shrink1.gro, 6400)
 does not match topology (topol.top, 6438)



6400 is the number of atoms in the 128-lipid DPPC bilayer (128 * 50 =
6400) so something has gone badly wrong here.  Your coordinate file at this
point should have the peptide and 126 lipids; the InflateGRO output below
looks correct. Check the contents of system_shrink1.gro and make sure you
haven't perhaps accidentally renamed a file something that it shouldn't be.

-Justin

I figured that since my number of molecules were off that the problem was

either the way I updated the molecules section of my topol.top fill by
adding
DPPC   126

after seeing this when adding lipids:

There are 128 lipids...
with 50 atoms per lipid..

Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet

Centering protein
Checking for overlap
...this might actually take a while
100 % done...
There are 2 lipids within cut-off range...
1 will be removed from the upper leaflet...
1 will be removed from the lower leaflet...

But for some reason I can't seem to start the EM iterations because of
this
error.

Sincerely,

Kyle Titus-Glover
Virginia Tech '17 | Engineering Science & Mechanics
Dean's Research Assistant, College of Engineering
443-802-4058



--
==

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

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

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

==
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--
==

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

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

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

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Re: [gmx-users] Gromacs 5.1 insert-molecules - Generating bad contacts?

[Dan Gil]

You are right!

Thank you.

On Mon, Jun 20, 2016 at 1:00 PM, Justin Lemkul  wrote:

>
>
> On 6/20/16 12:04 PM, Dan Gil wrote:
>
>> Hi Mark,
>>
>> I thought about your said, and tried to manage the VDW radi of atoms with
>> the "-radius" option.
>> I believe it scales the known VDW radi values by the number specified by
>> me. So I try:
>> "gmx insert-molecules ... ... -radius 1.2"
>>
>>  The result is still the same, I get segmentation errors because rms goes
>> to nan. I try again with "-radius 1.5" and I am still getting lucky.
>>
>>
> Your interpretation is incorrect.  See the help information, which
> explains:
>
> "A database (vdwradii.dat) of van der Waals
> radii is read by the program, and the resulting radii scaled by -scale. If
> radii are not found in the database, thoseatoms are assigned the
> (pre-scaled)
> distance -radius."
>
> Setting radii that large (over 1 nm) will probably make it hard for
> anything but the first few molecules to be inserted at all.
>
> -Justin
>
> Also, excuse me for creating a new question again. I was subscribed to
>> receive batch emails from the users-list, and I did not know how to
>> respond
>> questions in that mode.
>>
>> Thanks,
>>
>> Dan
>>
>>
> --
> ==
>
> 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
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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Re: [gmx-users] Tutorial 2: KALP-15 in DPPC

[Kyle Titus-Glover]

However, I did look into system_shrink1.gro and saw that the file was
missing the peptides and that 2 DPPC molecules still remained undeleted.
Should I manually correct the coordinate file?

On Mon, Jun 20, 2016 at 3:09 PM, Kyle Titus-Glover  wrote:

> I tried restarting the whole process to go back and carefully look and
> make sure that nothing was spelled right. Bu I still get the same error.
>
>
> On Mon, Jun 20, 2016 at 2:36 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 6/20/16 2:32 PM, Kyle Titus-Glover wrote:
>>
>>> Hey everyone,
>>>
>>> I've been working on the Justin Lemkul's 2nd tutorial and just can't seem
>>> to get past 2. packing the lipids around the protein and 3. solvating
>>> with
>>> water. The follow the instructions step by step but for some reason as I
>>> try to run EM  with
>>>
>>> gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp
>>>
>>> I get hit with this error:
>>>
>>> Fatal error:
>>> number of coordinates in coordinate file (system_shrink1.gro, 6400)
>>>  does not match topology (topol.top, 6438)
>>>
>>>
>> 6400 is the number of atoms in the 128-lipid DPPC bilayer (128 * 50 =
>> 6400) so something has gone badly wrong here.  Your coordinate file at this
>> point should have the peptide and 126 lipids; the InflateGRO output below
>> looks correct. Check the contents of system_shrink1.gro and make sure you
>> haven't perhaps accidentally renamed a file something that it shouldn't be.
>>
>> -Justin
>>
>> I figured that since my number of molecules were off that the problem was
>>> either the way I updated the molecules section of my topol.top fill by
>>> adding
>>> DPPC   126
>>>
>>> after seeing this when adding lipids:
>>>
>>> There are 128 lipids...
>>> with 50 atoms per lipid..
>>>
>>> Determining upper and lower leaflet...
>>> 64 lipids in the upper...
>>> 64 lipids in the lower leaflet
>>>
>>> Centering protein
>>> Checking for overlap
>>> ...this might actually take a while
>>> 100 % done...
>>> There are 2 lipids within cut-off range...
>>> 1 will be removed from the upper leaflet...
>>> 1 will be removed from the lower leaflet...
>>>
>>> But for some reason I can't seem to start the EM iterations because of
>>> this
>>> error.
>>>
>>> Sincerely,
>>>
>>> Kyle Titus-Glover
>>> Virginia Tech '17 | Engineering Science & Mechanics
>>> Dean's Research Assistant, College of Engineering
>>> 443-802-4058
>>>
>>>
>> --
>> ==
>>
>> 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
>>
>> ==
>> --
>> 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.
>>
>
>
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Re: [gmx-users] Tutorial 2: KALP-15 in DPPC

[Kyle Titus-Glover]

I tried restarting the whole process to go back and carefully look and make
sure that nothing was spelled right. Bu I still get the same error.


On Mon, Jun 20, 2016 at 2:36 PM, Justin Lemkul  wrote:

>
>
> On 6/20/16 2:32 PM, Kyle Titus-Glover wrote:
>
>> Hey everyone,
>>
>> I've been working on the Justin Lemkul's 2nd tutorial and just can't seem
>> to get past 2. packing the lipids around the protein and 3. solvating with
>> water. The follow the instructions step by step but for some reason as I
>> try to run EM  with
>>
>> gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp
>>
>> I get hit with this error:
>>
>> Fatal error:
>> number of coordinates in coordinate file (system_shrink1.gro, 6400)
>>  does not match topology (topol.top, 6438)
>>
>>
> 6400 is the number of atoms in the 128-lipid DPPC bilayer (128 * 50 =
> 6400) so something has gone badly wrong here.  Your coordinate file at this
> point should have the peptide and 126 lipids; the InflateGRO output below
> looks correct. Check the contents of system_shrink1.gro and make sure you
> haven't perhaps accidentally renamed a file something that it shouldn't be.
>
> -Justin
>
> I figured that since my number of molecules were off that the problem was
>> either the way I updated the molecules section of my topol.top fill by
>> adding
>> DPPC   126
>>
>> after seeing this when adding lipids:
>>
>> There are 128 lipids...
>> with 50 atoms per lipid..
>>
>> Determining upper and lower leaflet...
>> 64 lipids in the upper...
>> 64 lipids in the lower leaflet
>>
>> Centering protein
>> Checking for overlap
>> ...this might actually take a while
>> 100 % done...
>> There are 2 lipids within cut-off range...
>> 1 will be removed from the upper leaflet...
>> 1 will be removed from the lower leaflet...
>>
>> But for some reason I can't seem to start the EM iterations because of
>> this
>> error.
>>
>> Sincerely,
>>
>> Kyle Titus-Glover
>> Virginia Tech '17 | Engineering Science & Mechanics
>> Dean's Research Assistant, College of Engineering
>> 443-802-4058
>>
>>
> --
> ==
>
> 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
>
> ==
> --
> 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
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Re: [gmx-users] Tutorial 2: KALP-15 in DPPC

[Justin Lemkul]

On 6/20/16 2:32 PM, Kyle Titus-Glover wrote:

Hey everyone,

I've been working on the Justin Lemkul's 2nd tutorial and just can't seem
to get past 2. packing the lipids around the protein and 3. solvating with
water. The follow the instructions step by step but for some reason as I
try to run EM  with

gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp

I get hit with this error:

Fatal error:
number of coordinates in coordinate file (system_shrink1.gro, 6400)
 does not match topology (topol.top, 6438)



6400 is the number of atoms in the 128-lipid DPPC bilayer (128 * 50 = 6400) so 
something has gone badly wrong here.  Your coordinate file at this point should 
have the peptide and 126 lipids; the InflateGRO output below looks correct. 
Check the contents of system_shrink1.gro and make sure you haven't perhaps 
accidentally renamed a file something that it shouldn't be.


-Justin


I figured that since my number of molecules were off that the problem was
either the way I updated the molecules section of my topol.top fill by
adding
DPPC   126

after seeing this when adding lipids:

There are 128 lipids...
with 50 atoms per lipid..

Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet

Centering protein
Checking for overlap
...this might actually take a while
100 % done...
There are 2 lipids within cut-off range...
1 will be removed from the upper leaflet...
1 will be removed from the lower leaflet...

But for some reason I can't seem to start the EM iterations because of this
error.

Sincerely,

Kyle Titus-Glover
Virginia Tech '17 | Engineering Science & Mechanics
Dean's Research Assistant, College of Engineering
443-802-4058



--
==

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] charmm36 ions fix

[Justin Lemkul]

On 6/20/16 1:36 PM, gromacs query wrote:

My simulation cases are above 0.5 M (that is 500 mM) which are then higher
than as mentioned 100mM. Sorry I could not get when you say "correct
nonbonded settings". You mean vdW/electrostatic cutoff and switch/shift
etc. If it is the case then yes as am following proper mdp file taken from
some recent paper where they reproduce membrane properties but under normal
physiological salt conc. And also am using default CHARMM36 nonbonding
pairs with nbfix. Is there anything more to be considered?



Check and make sure:

http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM


So am wondering what should be done as I need to use above 0.5 M salt in
membrane-protein simulations.



Follow the analysis of the Venable paper to see if you're seeing any spurious 
interactions.  Perhaps what you're seeing is actually real, but if it's at odds 
with experimental data, then it's probably not (depending on the quality of the 
experimental data).


-Justin


Thanks for any suggestions.
JIomm

On Mon, Jun 20, 2016 at 6:23 PM, Justin Lemkul  wrote:




On 6/20/16 1:19 PM, gromacs query wrote:


Thanks Justin, basically am stuck with an old question of using high salt
conc. with membrane simulations and their dependence on force field
parameters versus experiments. Membrane thickness and area seems to be
sensitive to high salt at least in simulations.



Define "high."  The paper that derived and validated the lipid-ion NBFIX
terms only used up to 100 mM, so if you're going much beyond that, there
may be issues that need additional work.  The NBFIXes were validated using
osmotic pressure at much higher concentration, but membranes are, of
course, somewhat unique environments.

You're using the correct nonbonded settings, right?  The C36 lipids are
very sensitive to misuse...

-Justin


JIom


On Mon, Jun 20, 2016 at 5:35 PM, Justin Lemkul  wrote:




On 6/20/16 12:30 PM, gromacs query wrote:

Hi All,


I am using charmm36 downloaded from (MacKerell website). Somehow I was
enlightened while reading some papers applying NBFIX by Roux et al. I
can
see there is indeed a nbfix.itp file in CHARMM36 (not 27) and used as
default (via forcefield.itp) but the file does not mention any reference
where it comes from. I read the doc file but could not find reference
(sorry if missed it) or may be am missing the developmental stages thus
it
became quite a obvious thing. I am just wondering if nbfix.itp indeed
comes
from Roux et al.


We don't (really, can't possibly) provide all the references for all the

parameters in the C36 port.  That would require parsing all the comments
in
all of the CHARMM force field files.  Those are also freely available and
are the definitive source of all this information.

I assume you're referring to the SOD-CLA NBFIX?  That is indeed from Luo
and Roux JPCL 2010 (osmotic pressure calculations).  The same goes for
POT-CLA.

-Justin

--
==

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

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

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

==
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--
==

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

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

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

==
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--
==

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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* Please search

[gmx-users] Tutorial 2: KALP-15 in DPPC

[Kyle Titus-Glover]

Hey everyone,

I've been working on the Justin Lemkul's 2nd tutorial and just can't seem
to get past 2. packing the lipids around the protein and 3. solvating with
water. The follow the instructions step by step but for some reason as I
try to run EM  with

gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp

I get hit with this error:

Fatal error:
number of coordinates in coordinate file (system_shrink1.gro, 6400)
 does not match topology (topol.top, 6438)

I figured that since my number of molecules were off that the problem was
either the way I updated the molecules section of my topol.top fill by
adding
DPPC   126

after seeing this when adding lipids:

There are 128 lipids...
with 50 atoms per lipid..

Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet

Centering protein
Checking for overlap
...this might actually take a while
100 % done...
There are 2 lipids within cut-off range...
1 will be removed from the upper leaflet...
1 will be removed from the lower leaflet...

But for some reason I can't seem to start the EM iterations because of this
error.

Sincerely,

Kyle Titus-Glover
Virginia Tech '17 | Engineering Science & Mechanics
Dean's Research Assistant, College of Engineering
443-802-4058
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[gmx-users] Tutorial 2: KALP-15 in DPPC

[Kyle Titus-Glover]

Hey everyone,

I've been working on the Justin Lemkul's 2nd tutorial and just can't seem
to get past 2. packing the lipids around the protein and 3. solvating with
water. The follow the instructions step by step but for some reason as I
try to run EM  with

gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tp

I get hit with this error:

Fatal error:
number of coordinates in coordinate file (system_shrink1.gro, 6400)
 does not match topology (topol.top, 6438)

I figured that since my number of molecules were off that the problem was
either the way I updated the molecules section of my topol.top fill by
adding
DPPC   126

after seeing this when adding lipids:

There are 128 lipids...
with 50 atoms per lipid..

Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet

Centering protein
Checking for overlap
...this might actually take a while
100 % done...
There are 2 lipids within cut-off range...
1 will be removed from the upper leaflet...
1 will be removed from the lower leaflet...

But for some reason I can't seem to start the EM iterations because of this
error.

Sincerely,

Kyle Titus-Glover
Virginia Tech '17 | Engineering Science & Mechanics
Dean's Research Assistant, College of Engineering
443-802-4058
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[gmx-users] PCA

[sun]

Hello Users and Experts

Can anyone please suggest me good papers in which authors have performed 
principal component analysis and then projected the free energy landscape onto 
first two eigen vectors. I am confused as different studies give different 
results and used different parameters for same protein i.e. amyloid beta 
peptide monomer. Please help me.

With Regards
Suniba

Sent from my iPhone
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Re: [gmx-users] charmm36 ions fix

[gromacs query]

My simulation cases are above 0.5 M (that is 500 mM) which are then higher
than as mentioned 100mM. Sorry I could not get when you say "correct
nonbonded settings". You mean vdW/electrostatic cutoff and switch/shift
etc. If it is the case then yes as am following proper mdp file taken from
some recent paper where they reproduce membrane properties but under normal
physiological salt conc. And also am using default CHARMM36 nonbonding
pairs with nbfix. Is there anything more to be considered?

So am wondering what should be done as I need to use above 0.5 M salt in
membrane-protein simulations.

Thanks for any suggestions.
JIomm

On Mon, Jun 20, 2016 at 6:23 PM, Justin Lemkul  wrote:

>
>
> On 6/20/16 1:19 PM, gromacs query wrote:
>
>> Thanks Justin, basically am stuck with an old question of using high salt
>> conc. with membrane simulations and their dependence on force field
>> parameters versus experiments. Membrane thickness and area seems to be
>> sensitive to high salt at least in simulations.
>>
>>
> Define "high."  The paper that derived and validated the lipid-ion NBFIX
> terms only used up to 100 mM, so if you're going much beyond that, there
> may be issues that need additional work.  The NBFIXes were validated using
> osmotic pressure at much higher concentration, but membranes are, of
> course, somewhat unique environments.
>
> You're using the correct nonbonded settings, right?  The C36 lipids are
> very sensitive to misuse...
>
> -Justin
>
>
> JIom
>>
>> On Mon, Jun 20, 2016 at 5:35 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 6/20/16 12:30 PM, gromacs query wrote:
>>>
>>> Hi All,

 I am using charmm36 downloaded from (MacKerell website). Somehow I was
 enlightened while reading some papers applying NBFIX by Roux et al. I
 can
 see there is indeed a nbfix.itp file in CHARMM36 (not 27) and used as
 default (via forcefield.itp) but the file does not mention any reference
 where it comes from. I read the doc file but could not find reference
 (sorry if missed it) or may be am missing the developmental stages thus
 it
 became quite a obvious thing. I am just wondering if nbfix.itp indeed
 comes
 from Roux et al.


 We don't (really, can't possibly) provide all the references for all the
>>> parameters in the C36 port.  That would require parsing all the comments
>>> in
>>> all of the CHARMM force field files.  Those are also freely available and
>>> are the definitive source of all this information.
>>>
>>> I assume you're referring to the SOD-CLA NBFIX?  That is indeed from Luo
>>> and Roux JPCL 2010 (osmotic pressure calculations).  The same goes for
>>> POT-CLA.
>>>
>>> -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
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
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>>> posting!
>>>
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>>>
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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> 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] charmm36 ions fix

[Justin Lemkul]

On 6/20/16 1:19 PM, gromacs query wrote:

Thanks Justin, basically am stuck with an old question of using high salt
conc. with membrane simulations and their dependence on force field
parameters versus experiments. Membrane thickness and area seems to be
sensitive to high salt at least in simulations.



Define "high."  The paper that derived and validated the lipid-ion NBFIX terms 
only used up to 100 mM, so if you're going much beyond that, there may be issues 
that need additional work.  The NBFIXes were validated using osmotic pressure at 
much higher concentration, but membranes are, of course, somewhat unique 
environments.


You're using the correct nonbonded settings, right?  The C36 lipids are very 
sensitive to misuse...


-Justin


JIom

On Mon, Jun 20, 2016 at 5:35 PM, Justin Lemkul  wrote:




On 6/20/16 12:30 PM, gromacs query wrote:


Hi All,

I am using charmm36 downloaded from (MacKerell website). Somehow I was
enlightened while reading some papers applying NBFIX by Roux et al. I can
see there is indeed a nbfix.itp file in CHARMM36 (not 27) and used as
default (via forcefield.itp) but the file does not mention any reference
where it comes from. I read the doc file but could not find reference
(sorry if missed it) or may be am missing the developmental stages thus it
became quite a obvious thing. I am just wondering if nbfix.itp indeed
comes
from Roux et al.



We don't (really, can't possibly) provide all the references for all the
parameters in the C36 port.  That would require parsing all the comments in
all of the CHARMM force field files.  Those are also freely available and
are the definitive source of all this information.

I assume you're referring to the SOD-CLA NBFIX?  That is indeed from Luo
and Roux JPCL 2010 (osmotic pressure calculations).  The same goes for
POT-CLA.

-Justin

--
==

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

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

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

==
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--
==

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

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

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

==
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Re: [gmx-users] Basic Understanding about Gromacs C library

[Murilo Kramar]

Thanks for your answers and sorry for not describing my problem.


So, basically my problem is based on selections and some linear algebra
calculation. First of all I select a specific type of atoms and after that
I select a different group and calculate the angle of these atoms in
respect of a fixed point and other geometric properties.


If I'm correct I should use the '-selection' property by modifying this
struct (as in the second selection):


const char *mySel[] = {"name C"};


t_pargs pa[] = {

{"-cutoff", FALSE, etREAL, {&cutoff},

"Cutoff for distance calculation (0 = no cutoff)"},

{"-select", FALSE, etSTR, {mySel},

"Trying to do some selection"},

};


What I don't get is whether this selection is going to be passed to the
analyze_frame or not. Because if it does, then I need to do a further
selection that relies on the first one and I don't know how to proceed.


Thanks again,


Murilo.

On Fri, Jun 17, 2016 at 12:59 AM, David van der Spoel 
wrote:

> On 16/06/16 19:29, Murilo Kramar wrote:
>
>> Greetings, List,
>>
>> I have a set of data that I used to analyze through VMD. As the set is
>> quite heavy and there are many of them, using VMD was a bit cumbersome. So
>> it has been decided that working in GROMACS would present benefits.
>>
>> The first step that I executed was to compile via CentOs terminal  the
>> 'template.c' that comes with GROMACS 4.6.3 (the version that my group
>> works
>> with) in order to get used to its programming style. When it executes
>> there
>> is a 'header' telling some basic info about  the program (such as
>> command-line options used) and after that  I'm inquired to make selections
>> (to fill the -select option) . Where does this header come from? I'm
>> pretty
>> sure it is not coded directly in the 'template.c'. I ask this because I'm
>> trying to use the -select option inside the code, but it seems that I
>> can't
>> do that when I have this input asking.
>>
>
> You do not say what you are trying to analyze. Gromacs has many analysis
> tools ready to use.
>
>
>> I'm worried that this is a too simple question, but I'm really stuck at
>> this for 3 days. Pardon me if it is.
>>
>> Thanks in advance.
>>
>> Murilo G. K.
>> 
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>
> --
> Gromacs Users mailing list
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Re: [gmx-users] charmm36 ions fix

[gromacs query]

Thanks Justin, basically am stuck with an old question of using high salt
conc. with membrane simulations and their dependence on force field
parameters versus experiments. Membrane thickness and area seems to be
sensitive to high salt at least in simulations.

JIom

On Mon, Jun 20, 2016 at 5:35 PM, Justin Lemkul  wrote:

>
>
> On 6/20/16 12:30 PM, gromacs query wrote:
>
>> Hi All,
>>
>> I am using charmm36 downloaded from (MacKerell website). Somehow I was
>> enlightened while reading some papers applying NBFIX by Roux et al. I can
>> see there is indeed a nbfix.itp file in CHARMM36 (not 27) and used as
>> default (via forcefield.itp) but the file does not mention any reference
>> where it comes from. I read the doc file but could not find reference
>> (sorry if missed it) or may be am missing the developmental stages thus it
>> became quite a obvious thing. I am just wondering if nbfix.itp indeed
>> comes
>> from Roux et al.
>>
>>
> We don't (really, can't possibly) provide all the references for all the
> parameters in the C36 port.  That would require parsing all the comments in
> all of the CHARMM force field files.  Those are also freely available and
> are the definitive source of all this information.
>
> I assume you're referring to the SOD-CLA NBFIX?  That is indeed from Luo
> and Roux JPCL 2010 (osmotic pressure calculations).  The same goes for
> POT-CLA.
>
> -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
>
> ==
> --
> Gromacs Users mailing list
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> * Please search the archive at
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> posting!
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Re: [gmx-users] Gromacs 5.1 insert-molecules - Generating bad contacts?

[Justin Lemkul]

On 6/20/16 12:04 PM, Dan Gil wrote:

Hi Mark,

I thought about your said, and tried to manage the VDW radi of atoms with
the "-radius" option.
I believe it scales the known VDW radi values by the number specified by
me. So I try:
"gmx insert-molecules ... ... -radius 1.2"

 The result is still the same, I get segmentation errors because rms goes
to nan. I try again with "-radius 1.5" and I am still getting lucky.



Your interpretation is incorrect.  See the help information, which explains:

"A database (vdwradii.dat) of van der Waals
radii is read by the program, and the resulting radii scaled by -scale. If
radii are not found in the database, thoseatoms are assigned the (pre-scaled)
distance -radius."

Setting radii that large (over 1 nm) will probably make it hard for anything but 
the first few molecules to be inserted at all.


-Justin


Also, excuse me for creating a new question again. I was subscribed to
receive batch emails from the users-list, and I did not know how to respond
questions in that mode.

Thanks,

Dan



--
==

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] to neutralize the system

[Justin Lemkul]

On 6/19/16 11:03 AM, Alexander Alexander wrote:

Hello Mark,

I still need help choosing the right method of neutralization of my system.
I am wondering how the final states of the surface-binding process can shed
light on choosing the feasible method of neutralization, here, either
protonation (deprotonation) of amino acid and peptide or adding ions Na+
(Cl-)?



In the generic "charge neutralization" discussions here in recent days, people 
are talking about artifacts associated with using non-neutral simulation systems 
and relying on a uniform background charge from PME to "neutralize" these 
systems.  In some cases, the artifacts can be quite pronounced so counterions 
are a simple fix.


Neutralizing side chains has important physical consequences; you should choose 
the protonation state based on the actual physical properties of the system and 
the chemical environment (e.g. solution, the calculate pKa values of the 
species, etc).  Simply neutralizing side chains to fit a preconceived notion 
that the solute should be neutral (conflating the PME issues with real physical 
issues) is a dangerous road to go down.



For example, in one sample, I neutralized the Glutamic(zwitterionic form)
by protonating it and then in simulation, it gradually absorbed firstly to
the surface via one of the Hydrogen(C-H) in the end of the side chain, and
then laid steady down while NH3 group was pointing up.
In another sample, again I neutralized the Arginine(zwitterionic form) by
deprotonating it and then in simulation, it absorbed firstly to the surface
via the COO(-) group in the backbone, and then laid steady down similar to
the Glutamic.



Welcome to the challenge of using fixed charge/fixed topology simulations. 
Protonation states, in real systems, can vary.  Using traditional MD, they 
cannot.  There are methods to get around this (e.g. constant-pH simulations, but 
those are not - to my knowledge - readily available in GROMACS, though people 
have published wrapper-type approaches to doing this).


What you need to simulate is the most probable form of your peptides under 
whatever the solution condition is.  Deprotonating Arg requires crazily basic 
conditions, which may or may not be relevant to what you're studying.  Perhaps 
the protonation state does vary during the binding mechanism.  That's a 
challenge for you to address based on your knowledge of your specific system and 
published studies of similar systems.


-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] gmx rdf

[Justin Lemkul]

On 6/20/16 9:22 AM, amitbe...@chemeng.iisc.ernet.in wrote:

Hello gmx_users,
I was trying to plot distribution function in a bilayer system using gmx
rdf. I used the system as a reference ( thinking it will take the COM of
the system as reference point) . Then I plotted RDF of a marked atom. But
it is plotting only in the positive direction while the lipids in the
lower leaflet are also containing the marked atom. So I am unable to see
the distribution from center of the bilayer to the lower leaflet.
Can anyone please help me out in identifying my mistake.



Distance is a positive value and that's what gmx rdf will always report.  If you 
want to distinguish between different leaflets, create an index file for the 
different leaflets; but gmx rdf will always report a positive number.


-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] Restart to continue a free energy calculations

[Justin Lemkul]

On 6/20/16 9:40 AM, Alexander Alexander wrote:

Dear gromacs user,

My binding free energy calculation crashed while it was in the middle of
the one of the lambda_state because of the time limit, I was wondering if
it is possible to restart a crashed free energy calculation to continue
around crashed pont without loosing accuracy and information?

Or is it possible to extend a successfully compleated free energy
calculation for the longer time?



Should be.  Are you encountering any sort of problem, or is this all 
hypothetical?


I know that both of mentioned case are simply doable in a normal MD job.

Concerning to the precision of the new geromacs versions(e.g version 5.1.2)
, could you please confirm me that the Single, Mixed and double precision
are available or it is just Mixed and double precision?



GROMACS has been only mixed or double for many, many years.  The colloquial use 
of "single" precision is explained in the manual.


-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] charmm36 ions fix

[Justin Lemkul]

On 6/20/16 12:30 PM, gromacs query wrote:

Hi All,

I am using charmm36 downloaded from (MacKerell website). Somehow I was
enlightened while reading some papers applying NBFIX by Roux et al. I can
see there is indeed a nbfix.itp file in CHARMM36 (not 27) and used as
default (via forcefield.itp) but the file does not mention any reference
where it comes from. I read the doc file but could not find reference
(sorry if missed it) or may be am missing the developmental stages thus it
became quite a obvious thing. I am just wondering if nbfix.itp indeed comes
from Roux et al.



We don't (really, can't possibly) provide all the references for all the 
parameters in the C36 port.  That would require parsing all the comments in all 
of the CHARMM force field files.  Those are also freely available and are the 
definitive source of all this information.


I assume you're referring to the SOD-CLA NBFIX?  That is indeed from Luo and 
Roux JPCL 2010 (osmotic pressure calculations).  The same goes for POT-CLA.


-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] charmm36 ions fix

[gromacs query]

Hi All,

I am using charmm36 downloaded from (MacKerell website). Somehow I was
enlightened while reading some papers applying NBFIX by Roux et al. I can
see there is indeed a nbfix.itp file in CHARMM36 (not 27) and used as
default (via forcefield.itp) but the file does not mention any reference
where it comes from. I read the doc file but could not find reference
(sorry if missed it) or may be am missing the developmental stages thus it
became quite a obvious thing. I am just wondering if nbfix.itp indeed comes
from Roux et al.

Thanks for any suggestions.

JIom
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Re: [gmx-users] Gromacs 5.1 insert-molecules - Generating bad contacts?

[Dan Gil]

Hi Mark,

I thought about your said, and tried to manage the VDW radi of atoms with
the "-radius" option.
I believe it scales the known VDW radi values by the number specified by
me. So I try:
"gmx insert-molecules ... ... -radius 1.2"

 The result is still the same, I get segmentation errors because rms goes
to nan. I try again with "-radius 1.5" and I am still getting lucky.

Also, excuse me for creating a new question again. I was subscribed to
receive batch emails from the users-list, and I did not know how to respond
questions in that mode.

Thanks,

Dan
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Re: [gmx-users] PMF steadily increasing

[Christopher Neale]

Good that they are not interacting at large restraint distances. If they have 
opposite net charges, then one expects some attraction at any displacement, no 
matter how large. Obviously this attraction should decay into the noise at some 
distance, but I don't know how far that is and it should depend on salt 
concentration and also for your system the distribution of charges. For 
instance, if the nearest ends of the peptide and protein are 2 nm apart and 
have opposite net charge it would not surprise me at all if there was some 
attraction. If you can convince yourself that this is what is going on I 
presume that you could do some type of fit and extrapolation of the PMF that 
you do have.

I am worried about your comment that you are selecting frames. If you mean to 
start the run, then fine, but if you're scripting the selection of distances 
(frames) to use as wham input, then you've gone down the wrong track. My point 
about wham is that if you tell your wham program that the umbrella is centered 
at 6.0 nm but it is really centered at 6.05 nm then your going to get the wrong 
PMF and if there is any systematic bias between real center and what you tell 
wham then you would get a slope to your PMF.

I suggest that you do some test runs with (a) two LJ spheres and (b) with a 
Na-Cl pair. The first will help to confirm that you have no other error in your 
method and the second will give you a feel for separation distances at which 
the PMF flattens (and for your macromolecule analogy then you have to think in 
terms of the locations of point charges, not make the analogy to the center of 
mass).


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Lukas 
Zimmermann 
Sent: 20 June 2016 06:03:51
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] PMF steadily increasing

Thank you again for your remarks. This is what I found so far:

(1) With gmx mindist it was very clear that protein and peptide do not
interact. For the last 5 or 6 Umbrella Windows, the minimal distance
between the Pull groups was at least 2 nm
(2) That is indeed the case. The protein has net charge  -1 and the peptide
has charge +3.  Can you tell me what effect this might have?  I am unaware
that this might cause problems.
(3) I tried this, but this showed no apparent effect on the shape of the
curve.
(4) I do not understand in how far WHAM cares about the COM-COM distances.
I extract my frames from pull.xtc and I do not see each COM-COM distance
that would be required to have exactly, say, 0.1 nm
spacing, so I use a script which selects frames which resemble 0.1 nm
spacing as closely as possible, so there might some deviation.



2016-06-16 21:24 GMT+02:00 Lukas Zimmermann :

> Thank you very much for your suggestions. I will check your individual
> remarks and provide feedback.
>
> 2016-06-15 19:01 GMT+02:00 Christopher Neale  >:
>
>> (1) Are the protein and peptide really never interacting at d=7 nm? I
>> presume you've got a peptide that would be maybe 5 nm long when fully
>> extended, and your dG minimum is at 1.5 nm, so giving half the peptide
>> length that would imply possible contact at 4 nm, so I expect 7 nm is
>> sufficient, but gmx mindist can tell you for certain. For example, if the
>> protein forms an overhanging pocket around the binding site, then it is
>> quite possible that an unfolded peptide would be sometimes (even rarely)
>> contacting a 568 residue protein even at a COM-COM distance of 7 nm.
>>
>> (2) net charge positive on one and negative on the other?
>>
>> (3) unconverged? Did you try eliminating the first half of your
>> production sampling and see if this fixes the issue?
>>
>> (4) did you do wham properly? Your mdp file indicate that your windows
>> are not *exactly* at 0.1 and 0.2 nm increments (use of
>> pull_coord1_start=yes), which is fine but only as long as wham doesn't
>> think your windows are exactly at these increments.
>>
>> There may be some entropy change as the peptide becomes unbound and can
>> then sample full X and Y, but on its own that should not continue to impact
>> the sampling after contact is permanently broken.
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Lukas
>> Zimmermann 
>> Sent: 15 June 2016 12:45:51
>> To: gmx-us...@gromacs.org
>> Subject: [gmx-users] PMF steadily increasing
>>
>> Dear GROMACS community,
>>
>> I performed umbrella sampling study to estimate the binding free energy
>> between a globular
>> protein with 568 residues and a small peptide with 13 residues. I use the
>> pull code with k = 800 and rate = 0.005 to generate the initial
>> conformations over the time course of 1200 ps. The
>> center of masses distance between the pull groups ranges from  1.4 nm ad
>> 7.8 nm in the pull trajectory.
>>
>> I then extract conformations from pull.xtc with a spacing of 0.1 nm until
>> 3

Re: [gmx-users] converting the frcmod file and off file to gromacs

[Marlon Sidore]

Hi,

What you want is to convert these from amber (kcal) to gromacs (kJ). I
followed successfully another post from the mailing list here:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-September/101115.html

What you should do is make sure your conversion is right, by taking an
example from the amber forcefield in amber format and its equivalent in
gromacs format, before applying that conversion on your new parameters.

Hope that helps.

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France


2016-06-20 16:22 GMT+02:00 Mark Abraham :

> Hi,
>
> It sounds like what you want to look for is the documentation for those
> file formats.
>
> Mark
>
> On Sun, 19 Jun 2016 10:05 OuyangYanhua <15901283...@163.com> wrote:
>
> > Hi,
> > I am simulating a protein phosphorylated on Ser and Thr residues using
> > AMBER99SB-ILDN ff with Gromacs 5.0. I read the paper that I can use the
> > phophorylation parameters in the
> > http://sites.pharmacy.manchester.ac.uk/bryce/amber <
> > http://sites.pharmacy.manchester.ac.uk/bryce/amber> . However it is
> > difficult for me to read the parameters and statistics in the frcmod and
> > off files. So I have trouble in converting the statistics in framod files
> > and off file to gromacs files, such as .rtp, ffbond.itp.
> >
> > Best regards,
> > Ouyang
> > --
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Re: [gmx-users] converting the frcmod file and off file to gromacs

[Mark Abraham]

Hi,

It sounds like what you want to look for is the documentation for those
file formats.

Mark

On Sun, 19 Jun 2016 10:05 OuyangYanhua <15901283...@163.com> wrote:

> Hi,
> I am simulating a protein phosphorylated on Ser and Thr residues using
> AMBER99SB-ILDN ff with Gromacs 5.0. I read the paper that I can use the
> phophorylation parameters in the
> http://sites.pharmacy.manchester.ac.uk/bryce/amber <
> http://sites.pharmacy.manchester.ac.uk/bryce/amber> . However it is
> difficult for me to read the parameters and statistics in the frcmod and
> off files. So I have trouble in converting the statistics in framod files
> and off file to gromacs files, such as .rtp, ffbond.itp.
>
> Best regards,
> Ouyang
> --
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[gmx-users] Gaussian/GROMACS

[张 卓]

I am wondering who happened to have the experience to compile GROMACS with 
Gaussian09 so that Hybrid QM/MM could be achieved. I have read and downloaded 
the 'gau' script, but I am not sure if I would compile GROMACS with QMMM 
firstly. Would anyone give me some guide? I am using GROMACS 5.1.2. Thanks!



Zhuo

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[gmx-users] Restart to continue a free energy calculations

[Alexander Alexander]

Dear gromacs user,

My binding free energy calculation crashed while it was in the middle of
the one of the lambda_state because of the time limit, I was wondering if
it is possible to restart a crashed free energy calculation to continue
around crashed pont without loosing accuracy and information?

Or is it possible to extend a successfully compleated free energy
calculation for the longer time?

I know that both of mentioned case are simply doable in a normal MD job.

Concerning to the precision of the new geromacs versions(e.g version 5.1.2)
, could you please confirm me that the Single, Mixed and double precision
are available or it is just Mixed and double precision?

Thanks.

Regards,
Alex
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[gmx-users] gmx rdf

[amitbehra]

Hello gmx_users,
I was trying to plot distribution function in a bilayer system using gmx
rdf. I used the system as a reference ( thinking it will take the COM of
the system as reference point) . Then I plotted RDF of a marked atom. But
it is plotting only in the positive direction while the lipids in the
lower leaflet are also containing the marked atom. So I am unable to see
the distribution from center of the bilayer to the lower leaflet.
Can anyone please help me out in identifying my mistake.

Regards,
Amit Behera

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Re: [gmx-users] two protein

[Mark Abraham]

Hi,

Two kinds of protein is just like any two species - protein plus ligand
needs two moleculetype, one for each. Or protein plus water. The task is to
generate the moleculetype directives. This can be done immediately by
pdb2gmx, but there are other approaches.

Mark

On Mon, 20 Jun 2016 12:01 h.mousavi  wrote:

> Hi dear
> I want to consider the interaction of two proteins.
> How can I introduce two proteins in gromacs, simultaneously.
> 
> Seyed Habib allah Mousavi
> Assistant Professor of Physical Chemistry
> Dept. of Chemistry, College of Sciences
> Payame Noor University
> Jahrom, Iran
> 74176-8
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Re: [gmx-users] can we constrain a bond?

[Mark Abraham]

Hi,

There's kinds of bond type that implement such restraints. See chapter five.

Mark

On Mon, 20 Jun 2016 12:26 Albert  wrote:

> Hello:
>
> I noticed that we can use genrestr command line to restrain the atom
> position. I am just wondering is there any tools in Gromacs could be
> used for bond restrain? For instance: I would like to introduce some
> force constant for a ion coordinated bond.
>
> Thank you very much
>
> regards
>
> Albert
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[gmx-users] can we constrain a bond?

[Albert]

Hello:

I noticed that we can use genrestr command line to restrain the atom 
position. I am just wondering is there any tools in Gromacs could be 
used for bond restrain? For instance: I would like to introduce some 
force constant for a ion coordinated bond.


Thank you very much

regards

Albert
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Re: [gmx-users] PMF steadily increasing

[Lukas Zimmermann]

Thank you again for your remarks. This is what I found so far:

(1) With gmx mindist it was very clear that protein and peptide do not
interact. For the last 5 or 6 Umbrella Windows, the minimal distance
between the Pull groups was at least 2 nm
(2) That is indeed the case. The protein has net charge  -1 and the peptide
has charge +3.  Can you tell me what effect this might have?  I am unaware
that this might cause problems.
(3) I tried this, but this showed no apparent effect on the shape of the
curve.
(4) I do not understand in how far WHAM cares about the COM-COM distances.
I extract my frames from pull.xtc and I do not see each COM-COM distance
that would be required to have exactly, say, 0.1 nm
spacing, so I use a script which selects frames which resemble 0.1 nm
spacing as closely as possible, so there might some deviation.



2016-06-16 21:24 GMT+02:00 Lukas Zimmermann :

> Thank you very much for your suggestions. I will check your individual
> remarks and provide feedback.
>
> 2016-06-15 19:01 GMT+02:00 Christopher Neale  >:
>
>> (1) Are the protein and peptide really never interacting at d=7 nm? I
>> presume you've got a peptide that would be maybe 5 nm long when fully
>> extended, and your dG minimum is at 1.5 nm, so giving half the peptide
>> length that would imply possible contact at 4 nm, so I expect 7 nm is
>> sufficient, but gmx mindist can tell you for certain. For example, if the
>> protein forms an overhanging pocket around the binding site, then it is
>> quite possible that an unfolded peptide would be sometimes (even rarely)
>> contacting a 568 residue protein even at a COM-COM distance of 7 nm.
>>
>> (2) net charge positive on one and negative on the other?
>>
>> (3) unconverged? Did you try eliminating the first half of your
>> production sampling and see if this fixes the issue?
>>
>> (4) did you do wham properly? Your mdp file indicate that your windows
>> are not *exactly* at 0.1 and 0.2 nm increments (use of
>> pull_coord1_start=yes), which is fine but only as long as wham doesn't
>> think your windows are exactly at these increments.
>>
>> There may be some entropy change as the peptide becomes unbound and can
>> then sample full X and Y, but on its own that should not continue to impact
>> the sampling after contact is permanently broken.
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Lukas
>> Zimmermann 
>> Sent: 15 June 2016 12:45:51
>> To: gmx-us...@gromacs.org
>> Subject: [gmx-users] PMF steadily increasing
>>
>> Dear GROMACS community,
>>
>> I performed umbrella sampling study to estimate the binding free energy
>> between a globular
>> protein with 568 residues and a small peptide with 13 residues. I use the
>> pull code with k = 800 and rate = 0.005 to generate the initial
>> conformations over the time course of 1200 ps. The
>> center of masses distance between the pull groups ranges from  1.4 nm ad
>> 7.8 nm in the pull trajectory.
>>
>> I then extract conformations from pull.xtc with a spacing of 0.1 nm until
>> 3
>> nm distance
>> and a spacing of 0.2 nm for the remainder, yielding 38 windows in total.
>> After having
>> equilibrated each window with NVT and NPT under full position restraints,
>> I
>> conducted
>> production simulation under NPT ensemble for 14 ns for each window.
>> Finally, gmx wham
>> computed the PMF curve which you can see here:
>>
>> https://www.dropbox.com/s/fp7ol41qoyokmjm/profile.xvg?dl=0
>>
>> and this is the associated histogram:
>>
>> https://www.dropbox.com/s/bp6obymjc2qeu37/histo.xvg?dl=0
>>
>> Please find here my MDP pull parameters:
>>
>> pull= yes
>> pull_ngroups= 2
>> pull_ncoords= 1
>> pull_group1_name= chainB; Protein
>> pull_group2_name= chainC; Peptide
>> pull_coord1_type= umbrella
>> pull_coord1_geometry= distance
>> pull_coord1_groups  = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_rate= 0.0
>> pull_coord1_k   = 800
>> pull_coord1_start   = yes
>>
>>
>> I would now be very interested why the curve does not become flat beyond
>> some certain distance, but rather seems to increase in a linear fashion,
>> though the distance between the pull groups is sufficiently large. Could
>> this be related to entropic effects? Is there a way to
>> have the PMF properly normalized?
>>
>> The force field here is GROMOS 53a6 with SPC water. Temperature is coupled
>> to
>> 310 K and pressure to 1 bar.  Cutoffs are 1.4 nm, longe range ES are
>> resolved with PME
>> and DispCorr is set to EnerPress. Bonds are constrained with LINCS.
>>
>> The Protein is prevented from rotation by having three CA atoms restrained
>> with FC 1000.
>>
>>
>> Thank you very much, I appreciate any help and suggestions.
>>
>> Lukas
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Suppor

[gmx-users] two protein

[h.mousavi]

Hi dear
I want to consider the interaction of two proteins.
How can I introduce two proteins in gromacs, simultaneously.

Seyed Habib allah Mousavi
Assistant Professor of Physical Chemistry
Dept. of Chemistry, College of Sciences
Payame Noor University
Jahrom, Iran
74176-8
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