Re: [gmx-users] CHARMM36 parameter for polysaccharide branching

[Mohammad Hassan Khatami]

Thanks Justin :) 
It worked.
Small numbers!!!
Best,
MH
> On May 25, 2017, at 3:29 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 5/25/17 3:00 PM, Mohammad Hassan Khatami wrote:
>> Hello!
>> I am trying to simulate a simple branching polysaccharide molecule. Thanks 
>> to you, I found and implemented the CHARMM36 parameters for the 1->4 and 
>> 1->6 links, however, I was not able to find the exact partial charge 
>> parameters for the monomer in the branching point of the polymer. In other 
>> words, I am looking for parameters for the monomer AAA(the name is 
>> arbitrary), below:
>> 
>> 1->6 —AGM—1->4—AGF
>>/
>> AGI—1->4—AAA—1->4—AGF
>> 
>> I have combined the parameters for 1->4 (14ba) and 1->6(16ab) links from 
>> top_all36_carb.rtf  and the simulation is running with all bonds and links 
>> in place, but the total charge of the system is not zero (which it should). 
>> My only concern is if specific parameters for the monomer in the branching 
>> point of the polymer, exists, and where can I find them?
>> 
> 
> The same place as you got the linkages; all the PRES entries I pointed out 
> before (as well as the 1-6 linkages) have the correct charges and types 
> specified.  Your charge should come out to net neutral, as the branching 
> doesn't impose any net charge.  Check your work carefully.
> 
> -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] RMSF per residue

[Mohsen Ramezanpour]

Thanks Justin!

On Thu, May 25, 2017 at 12:54 PM, Justin Lemkul  wrote:

>
>
> On 5/24/17 4:12 PM, Mohsen Ramezanpour wrote:
>
>> Dear Gromacs users,
>>
>> I have a question on RMSF calculation:
>>
>> I am not sure how -res works in RMSF and I could not find any useful
>> explanation for it.
>>
>> It will give the average fluctuations per residue, fine. but how exactly?
>>
>> 1) it calculates the RMSF for each atom in that residue first. Then, it
>> averages over all of these atoms and reports it as the average for the
>> residue.
>>
>> 2) it takes the center of mass or specific atom of the residue and
>> calculates the RMSF for that.
>>
>> Or something else?
>>
>>
>> I am interested in the average fluctuation for sidechain of one residue
>> (excluding H atoms from this calculation). I want to have only one value
>> as
>> the average fluctuation for this group.
>>
>> I choose the residue-sidechain-H group (which I made in an index file)
>> when
>> prompted in the following command:
>>
>> gmx rmsf  -f  md.xtc  -fit   -s  md.tpr   -n index.ndx  -o
>>  residues-sidechain-H.xvg  -res
>>
>>
>> an alternative would be to use the following command and make an average
>> over all atoms manually:
>>
>> gmx rmsf  -f  md.xtc  -fit   -s  md.tpr   -n index.ndx  -o
>>  residues-sidechain-H.xvg
>>
>>
>> The results are NOT the same as expected. I think I should use the second
>> command and make the average manually. What do you think?
>>
>>
> The total RMSF of the selection is computed, then a mass-weighted average
> over each of the atoms is computed and that subsequent value assigned for
> output. See the "average_residues" function in
> src/gromacs/gmxana/gmx_rmsf.cpp
>
> -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] simulating AMP covalently linked to a protein

[Justin Lemkul]

On 5/25/17 3:12 PM, Gilberto Valdes wrote:

Thanks for your answer,
I would like to use charmm27 force field, it covers the hole AMP molecule
if I use the ADE residue with the 5PHO and 3TER patches implemented in
charmm software.
The problem is how to patch the ADE equivalent residue (named RA) in
gromacs, and then how to linked to the epsilon N group of the Lys.


Use our CHARMM36 port:

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

It has ATP, from which you can easily make an AMP unit linked to lysine.  You'll 
likely have to parametrize the linkage.  This will involve a geometry 
optimization, charge assignment (most can be taken by analogy, just a few atoms 
around the linkage should change), water interactions, a bonded refinement 
including potential energy scans for dihedrals.  You can probably use CGenFF as 
a starting point but you should ultimately not mix general atom types with 
protein and nucleic acid types.


-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 parameter for polysaccharide branching

[Justin Lemkul]

On 5/25/17 3:00 PM, Mohammad Hassan Khatami wrote:

Hello!
I am trying to simulate a simple branching polysaccharide molecule. Thanks to you, I 
found and implemented the CHARMM36 parameters for the 1->4 and 1->6 links, 
however, I was not able to find the exact partial charge parameters for the monomer 
in the branching point of the polymer. In other words, I am looking for parameters 
for the monomer AAA(the name is arbitrary), below:

 1->6 —AGM—1->4—AGF
/
AGI—1->4—AAA—1->4—AGF

I have combined the parameters for 1->4 (14ba) and 1->6(16ab) links from 
top_all36_carb.rtf  and the simulation is running with all bonds and links in place, 
but the total charge of the system is not zero (which it should). My only concern is 
if specific parameters for the monomer in the branching point of the polymer, exists, 
and where can I find them?



The same place as you got the linkages; all the PRES entries I pointed out 
before (as well as the 1-6 linkages) have the correct charges and types 
specified.  Your charge should come out to net neutral, as the branching doesn't 
impose any net charge.  Check your work carefully.


-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] simulating AMP covalently linked to a protein

[Gilberto Valdes]

Thanks for your answer,
I would like to use charmm27 force field, it covers the hole AMP molecule
if I use the ADE residue with the 5PHO and 3TER patches implemented in
charmm software.
The problem is how to patch the ADE equivalent residue (named RA) in
gromacs, and then how to linked to the epsilon N group of the Lys.
greets Gilberto

2017-05-25 13:55 GMT-05:00 Justin Lemkul :

>
>
> On 5/24/17 7:08 PM, Gilberto Valdes wrote:
>
>> Hi,
>>
>> I'm interested in simulating a DNA ligase with an AMP bound covalently via
>> its P atom to the side chain of a Lysine residue. I can not find any
>> parameters for that. I really appreciate any help in how to achieve this.
>>
>>
> http://www.gromacs.org/Documentation/How-tos/Parameterization
>
> The details depend on which force field you've chosen to use, and that
> choice actually depends on other factors - how much chemical space that
> force field covers (e.g. how easy is it going to be to even start this
> venture) and how easy to follow are the published methods for that force
> field.
>
> -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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[gmx-users] CHARMM36 parameter for polysaccharide branching

[Mohammad Hassan Khatami]

Hello!
I am trying to simulate a simple branching polysaccharide molecule. Thanks to 
you, I found and implemented the CHARMM36 parameters for the 1->4 and 1->6 
links, however, I was not able to find the exact partial charge parameters for 
the monomer in the branching point of the polymer. In other words, I am looking 
for parameters for the monomer AAA(the name is arbitrary), below:

 1->6 —AGM—1->4—AGF
/
AGI—1->4—AAA—1->4—AGF

I have combined the parameters for 1->4 (14ba) and 1->6(16ab) links from 
top_all36_carb.rtf  and the simulation is running with all bonds and links in 
place, but the total charge of the system is not zero (which it should). My 
only concern is if specific parameters for the monomer in the branching point 
of the polymer, exists, and where can I find them?

Best,
MH

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Re: [gmx-users] DSSP

[Justin Lemkul]

On 5/25/17 12:08 PM, Mariusz Wierzbowski wrote:

Hi,

I would like to analyze secondary structure elements for my protein. I want to
do it with do_dssp command in gromacs. I am using gromacs on a plgrid platform.
The problem is that an error occurs:

Fatal error: DSSP executable (/opt/dssp/bin/dssp) does not exist (use setenv 
DSSP).

On other forums I have read about setting the environment with setenv or export
DSSP
but I think that these solutions are for programs on local system.



do_dssp is just a wrapper that calls the dssp program.  do_dssp always needs to 
know where the dssp binary is and it does that by assuming it is in 
/usr/local/bin/dssp unless you specify otherwise with an environment variable. 
That's true no matter what kind of computer you're running on.


-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] em and nvt problem

[Justin Lemkul]

On 5/25/17 7:12 AM, Kashif wrote:

Hi
Whenever I tried to simulate one of my docked complex, the energy
minimization step converged very fast and complete at 112 steps. And when I
proceed with NVT equilibration I got split structures like 
step4b_n6.pdb
step4c_n6.pdb
step5b_n6.pdb
step5c_n6.pdb

I have already docked the drug with my protein using different tool in
order to get different docked pose of drug. So that I could get different
topology file and coordinate file of the drug from PRODRG server.


PRODRG generates topologies that are of insufficient quality for MD simulations, 
unless you significantly refine them.  Use better tools like ATB or another 
force field that has robust parametrization tools or easy-to-follow protocols.


Your system isn't stable, and I'd look at the ligand topology as the source of 
that instability, but do follow 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System


-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] Check stability of complex

[Justin Lemkul]

On 5/25/17 5:19 AM, Kashif wrote:

Hi
I have simulated my protein drug complex for 20 ns. My protein size was
actually 600 amino acid residues but I have simulated only docked portion
of my protein which was only about 300 aa residues. Now I want to see the
effect of rest of my protein sequences on the stability of this 300 aa+drug
complex.
How to do that?



Simulating the whole 600-residue protein is where I'd start.

-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] gromacs bond energy calculate

[Justin Lemkul]

On 5/25/17 3:57 AM, 王珍 wrote:

Hi all,
Recently i want to cauculate the bond energy and angle energy for my RNA 
system, and the RNA was simulated by gromacs about 100 ns, could I use the 
command of gromacs to calculate the bond energy and angle energy for the RNA 
residues in my all-atom molecular dynamics simulation? Thank you very much!


Use convert-tpr to create a subset .tpr file that contains only RNA, and use 
trjconv to create a trajectory that contains only RNA.  Then supply those files 
to mdrun -rerun to recalculate the energies.


-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] simulating AMP covalently linked to a protein

[Justin Lemkul]

On 5/24/17 7:08 PM, Gilberto Valdes wrote:

Hi,

I'm interested in simulating a DNA ligase with an AMP bound covalently via
its P atom to the side chain of a Lysine residue. I can not find any
parameters for that. I really appreciate any help in how to achieve this.



http://www.gromacs.org/Documentation/How-tos/Parameterization

The details depend on which force field you've chosen to use, and that choice 
actually depends on other factors - how much chemical space that force field 
covers (e.g. how easy is it going to be to even start this venture) and how easy 
to follow are the published methods for that force field.


-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] RMSF per residue

[Justin Lemkul]

On 5/24/17 4:12 PM, Mohsen Ramezanpour wrote:

Dear Gromacs users,

I have a question on RMSF calculation:

I am not sure how -res works in RMSF and I could not find any useful
explanation for it.

It will give the average fluctuations per residue, fine. but how exactly?

1) it calculates the RMSF for each atom in that residue first. Then, it
averages over all of these atoms and reports it as the average for the
residue.

2) it takes the center of mass or specific atom of the residue and
calculates the RMSF for that.

Or something else?


I am interested in the average fluctuation for sidechain of one residue
(excluding H atoms from this calculation). I want to have only one value as
the average fluctuation for this group.

I choose the residue-sidechain-H group (which I made in an index file) when
prompted in the following command:

gmx rmsf  -f  md.xtc  -fit   -s  md.tpr   -n index.ndx  -o
 residues-sidechain-H.xvg  -res


an alternative would be to use the following command and make an average
over all atoms manually:

gmx rmsf  -f  md.xtc  -fit   -s  md.tpr   -n index.ndx  -o
 residues-sidechain-H.xvg


The results are NOT the same as expected. I think I should use the second
command and make the average manually. What do you think?



The total RMSF of the selection is computed, then a mass-weighted average over 
each of the atoms is computed and that subsequent value assigned for output. 
See the "average_residues" function in src/gromacs/gmxana/gmx_rmsf.cpp


-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] Nose-Hoover + acc-grps

[jwillcox]

Hello,

I'm trying to run non-equilibrium simulations in the NVT ensemble with the
"acc-grps" command and the Nose-Hoover thermostat, but I know that there
are ways in which an external acceleration can be incompatible with
Nose-Hoover.  Are these two compatible in the Gromacs code?

Thank you,

Jon

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[gmx-users] DSSP

[Mariusz Wierzbowski]

Hi,

I would like to analyze secondary structure elements for my protein. I want 
to do it with do_dssp command in gromacs. I am using gromacs on a plgrid 
platform. The problem is that an error occurs:


Fatal error: DSSP executable (/opt/dssp/bin/dssp) does not exist (use setenv 
DSSP).


On other forums I have read about setting the environment with setenv or 
export DSSP

but I think that these solutions are for programs on local system.

I would appreciate any help. Thanks.

Best regards

Mariusz

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Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

[Szilárd Páll]

On Thu, May 25, 2017 at 2:09 PM, Marcelo Depólo  wrote:
> Hi,
>
>
> I had the same struggle benchmarking a similar system last week. Just for
> curiosity, could you tell us the performance you get when sharing your GPU
> with multiple jobs?

BTW, interpreting some performance number is not not always
straightforward as it depends on both CPU/GPU hardware, type of
simulation and settings and it will vary somewhat GROMACS release (the
last release brought several related improvements).

As examples/references you can have a look at these results:
Slide 56 of https://goo.gl/7DnSri
Fig 5 of http://doi.wiley.com/10.1002/jcc.24030  (or
http://arxiv.org/abs/1507.00898)

Therefore, I suggest that you try it yourself, if you have multiple
runs to do either sequentially or all in parallel, try 1-8-way
concurrency (given your 8-core CPU) and pick what's best for you!

Cheers,
--
Szilárd

>
> In my case (6k atoms + Reaction field + 8 cores 2.2Ghz + TitanX Pascal),
> I've got ~440 ns/day. However, I get ~280 ns/day running 2 jobs and sharing
> the GPU.
>
> Cheers!
> --
> Marcelo
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Re: [gmx-users] em and nvt problem

[Marlon Sidore]

You can try to reduce emtol in your minimization parameters or start your
nvt at a different, lower, temperature.

Best,

Marlon Sidore


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


2017-05-25 15:05 GMT+02:00 Daniel Kozuch :

> It would be helpful if you include the output of the em run and the log
> file for the nvt run.
>
> Best,
> Dan
>
> On Thu, May 25, 2017 at 7:12 AM, Kashif 
> wrote:
>
> > Hi
> > Whenever I tried to simulate one of my docked complex, the energy
> > minimization step converged very fast and complete at 112 steps. And
> when I
> > proceed with NVT equilibration I got split structures like 
> > step4b_n6.pdb
> > step4c_n6.pdb
> > step5b_n6.pdb
> > step5c_n6.pdb
> >
> > I have already docked the drug with my protein using different tool in
> > order to get different docked pose of drug. So that I could get different
> > topology file and coordinate file of the drug from PRODRG server.
> > But the same problem encounters.
> > Some time I got the error like .
> >
> > Fatal error:
> > 1 particles communicated to PME node 5 are more than 2/3 times the
> cut-off
> > out of the domain decomposition cell of their charge group in dimension
> y.
> > This usually means that your system is not well equilibrated.
> > 
> >
> > kindly help
> >
> > regards
> > kashif
> > --
> > Gromacs Users mailing list
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Re: [gmx-users] em and nvt problem

[Daniel Kozuch]

It would be helpful if you include the output of the em run and the log
file for the nvt run.

Best,
Dan

On Thu, May 25, 2017 at 7:12 AM, Kashif  wrote:

> Hi
> Whenever I tried to simulate one of my docked complex, the energy
> minimization step converged very fast and complete at 112 steps. And when I
> proceed with NVT equilibration I got split structures like 
> step4b_n6.pdb
> step4c_n6.pdb
> step5b_n6.pdb
> step5c_n6.pdb
>
> I have already docked the drug with my protein using different tool in
> order to get different docked pose of drug. So that I could get different
> topology file and coordinate file of the drug from PRODRG server.
> But the same problem encounters.
> Some time I got the error like .
>
> Fatal error:
> 1 particles communicated to PME node 5 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension y.
> This usually means that your system is not well equilibrated.
> 
>
> kindly help
>
> regards
> kashif
> --
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Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

[Szilárd Páll]

On Thu, May 25, 2017 at 2:09 PM, Marcelo Depólo  wrote:
> Hi,
>
>
> I had the same struggle benchmarking a similar system last week. Just for
> curiosity, could you tell us the performance you get when sharing your GPU
> with multiple jobs?
>
> In my case (6k atoms + Reaction field + 8 cores 2.2Ghz + TitanX Pascal),
> I've got ~440 ns/day. However, I get ~280 ns/day running 2 jobs and sharing
> the GPU.

I guess you mean 440 ns/day vs 2x280 ns/day. With RF (as the CPU is
waiting for the GPU not having any PME work to do) you might see even
better aggregate performance with more jobs sharing a GPU.

>
> Cheers!
> --
> Marcelo
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Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

[Daniel Kozuch]

Hi Marcelo,

That sounds reasonable depending on your time-step and other factors, but I
have not attempted to run with more than one job for GPU.
Maybe Mark can comment more.

Best,
Dan

On Thu, May 25, 2017 at 8:09 AM, Marcelo Depólo 
wrote:

> Hi,
>
>
> I had the same struggle benchmarking a similar system last week. Just for
> curiosity, could you tell us the performance you get when sharing your GPU
> with multiple jobs?
>
> In my case (6k atoms + Reaction field + 8 cores 2.2Ghz + TitanX Pascal),
> I've got ~440 ns/day. However, I get ~280 ns/day running 2 jobs and sharing
> the GPU.
>
> Cheers!
> --
> Marcelo
> --
> 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] Poor GPU Performance with GROMACS 5.1.4

[Marcelo Depólo]

Hi,


I had the same struggle benchmarking a similar system last week. Just for
curiosity, could you tell us the performance you get when sharing your GPU
with multiple jobs?

In my case (6k atoms + Reaction field + 8 cores 2.2Ghz + TitanX Pascal),
I've got ~440 ns/day. However, I get ~280 ns/day running 2 jobs and sharing
the GPU.

Cheers!
--
Marcelo
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[gmx-users] em and nvt problem

[Kashif]

Hi
Whenever I tried to simulate one of my docked complex, the energy
minimization step converged very fast and complete at 112 steps. And when I
proceed with NVT equilibration I got split structures like 
step4b_n6.pdb
step4c_n6.pdb
step5b_n6.pdb
step5c_n6.pdb

I have already docked the drug with my protein using different tool in
order to get different docked pose of drug. So that I could get different
topology file and coordinate file of the drug from PRODRG server.
But the same problem encounters.
Some time I got the error like .

Fatal error:
1 particles communicated to PME node 5 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.


kindly help

regards
kashif
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[gmx-users] Check stability of complex

[Kashif]

Hi
I have simulated my protein drug complex for 20 ns. My protein size was
actually 600 amino acid residues but I have simulated only docked portion
of my protein which was only about 300 aa residues. Now I want to see the
effect of rest of my protein sequences on the stability of this 300 aa+drug
complex.
How to do that?

thanks


regards
k
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Re: [gmx-users] gromacs bond energy calculate

[Dawid das]

Hi Jane,
I don't know if you can do that with one of Gromacs tools, but you can
easily extract your bond length/angle values
as a function of time with gmx distance and gmx angle, respectively.
Then, knowing the formula for bond and angle energies as well as parameters
(force constants and reference values)
you can write your own script that calculates the energy.

Best wishes,
Dawid

2017-05-25 9:57 GMT+02:00 王珍 <348363...@qq.com>:

> Hi all,
> Recently i want to cauculate the bond energy and angle energy for my
> RNA system, and the RNA was simulated by gromacs about 100 ns, could I use
> the command of gromacs to calculate the bond energy and angle energy for
> the RNA residues in my all-atom molecular dynamics simulation? Thank you
> very much!
> jane
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[gmx-users] gromacs bond energy calculate

[????]

Hi all,
Recently i want to cauculate the bond energy and angle energy for my RNA 
system, and the RNA was simulated by gromacs about 100 ns, could I use the 
command of gromacs to calculate the bond energy and angle energy for the RNA 
residues in my all-atom molecular dynamics simulation? Thank you very much!
jane
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Re: [gmx-users] gromacs-5.1.4 installation issue

[Mark Abraham]

Hi,

Yes, those are from the standard system compiler, which obviously doesn't
work. You're not using that compiler, so you need to know how the one you
are using should be used and where its standard library is and why the
clusters are not actually identical because one compiler works and one
doesn't ;-) That means talking to the people who set them up. For example,
you forgot to load the module one time. Or one module sets LD_LIBRARY_PATH
and one does not.

Mark


On Thu, May 25, 2017 at 8:41 AM abhisek Mondal 
wrote:

> On Wed, May 24, 2017 at 6:08 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > You should ask the cluster maintainers how they intend the compiler to be
> > used. You need to find the same infrastructure at run time as you used at
> > compile time, e.g. by loading the same modules.
> >
> > Yes I did check.
> I have 2 cluster with identical configurations. In Cluster_1 it compiled
> well and running nicely.
> But in Cluster_2 it is giving this error.
>
> To check the GLIBCXX version available in both Clusters, we used: strings
> /usr/lib/libstdc++.so.6 | grep GLIBCXX
> Output of BOTH clusters:
> GLIBCXX_3.4
> GLIBCXX_3.4.1
> GLIBCXX_3.4.2
> GLIBCXX_3.4.3
> GLIBCXX_3.4.4
> GLIBCXX_3.4.5
> GLIBCXX_3.4.6
> GLIBCXX_3.4.7
> GLIBCXX_3.4.8
> GLIBCXX_3.4.9
> GLIBCXX_3.4.10
> GLIBCXX_3.4.11
> GLIBCXX_3.4.12
> GLIBCXX_3.4.13
> GLIBCXX_FORCE_NEW
> GLIBCXX_DEBUG_MESSAGE_LENGTH
>
> So, I'm confused regarding both the machine does not have  `GLIBCXX_3.4.15`
> , then why in one machine /gromacs-5.1.4/lib64/libgromacs_mpi.so.1 is
> raising error but not in the other ?
>
> Is there any way to overcome this ? I'm really confused.
>
> Some advice regarding this concern will be highly appreciated.
>
> Thank you.
>
>
>
> > Mark
> >
> > On Wed, May 24, 2017 at 2:13 PM abhisek Mondal 
> > wrote:
> >
> > > Hi,
> > >
> > >I have been trying to install latest version of gromacs
> > (Gromacs-5.1.4)
> > > in my cluster.
> > >
> > > Installation went without any error. But whenever I'm giving the
> command:
> > > gmx_mpi
> > > An error report comes:
> > > gmx_mpi: /lib64/libz.so.1: no version information available (required
> by
> > > /app/gromacs-5.1.4/lib64/libgromacs_mpi.so.1)
> > > gmx_mpi: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found
> > > (required by /app/gromacs-5.1.4/lib64/libgromacs_mpi.so.1)
> > >
> > >
> > > Can you please help me out here, regarding what is going wrong here.
> > >
> > > Thank you.
> > >
> > > --
> > > Abhisek Mondal
> > >
> > > *Senior Research Fellow*
> > >
> > > *Structural Biology and Bioinformatics Division*
> > > *CSIR-Indian Institute of Chemical Biology*
> > >
> > > *Kolkata 700032*
> > >
> > > *INDIA*
> > > --
> > > Gromacs Users mailing list
> > >
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> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
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> > >
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> >
>
>
>
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
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Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

[Mark Abraham]

Hi,

Good. Remember that the job scheduler is a degree of freedom that matters,
so how you used it and why would have been good to mention the first time
;-) And don't just set your time step to arbitrary numbers unless you know
why it is a stable integration scheme.

Mark

On Thu, May 25, 2017 at 4:48 AM Daniel Kozuch  wrote:

> I apologize for the confusion, but I found my error. I was failing to
> request a certain number of cpus-per-task and the scheduler was having
> issues assigning the threads because of this. Speed is now at ~400 ns/day
> with a 3 fs timestep which seems reasonable.
>
> Thanks for all the help,
> Dan
>
> On Wed, May 24, 2017 at 9:48 PM, Daniel Kozuch 
> wrote:
>
> > Szilárd,
> >
> > I think I must be misunderstanding your advice. If I remove the domain
> > decomposition and set pin on as suggested by Mark, using:
> >
> > gmx_gpu mdrun -deffnm my_tpr -dd 1 -pin on
> >
> > Then I get very poor performance and the following error:
> >
> > NOTE: Affinity setting for 6/6 threads failed. This can cause performance
> > degradation.
> >   If you think your settings are correct, ask on the gmx-users list.
> >
> > I am running only one rank and using 6 threads (I do not want to use all
> > the available 28 cores on the node because I hope to run multiple of
> these
> > jobs per node in the near future).
> >
> > Thanks for the help,
> > Dan
> >
> >
> > 
> > -
> > Log File:
> >
> > GROMACS version:VERSION 5.1.4
> > Precision:  single
> > Memory model:   64 bit
> > MPI library:MPI
> > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
> > GPU support:enabled
> > OpenCL support: disabled
> > invsqrt routine:gmx_software_invsqrt(x)
> > SIMD instructions:  AVX2_256
> > FFT library:fftw-3.3.4-sse2-avx
> > RDTSCP usage:   enabled
> > C++11 compilation:  disabled
> > TNG support:enabled
> > Tracing support:disabled
> > Built on:   Mon May 22 18:29:21 EDT 2017
> > Built by:   dkoz...@tigergpu.princeton.edu [CMAKE]
> > Build OS/arch:  Linux 3.10.0-514.16.1.el7.x86_64 x86_64
> > Build CPU vendor:   GenuineIntel
> > Build CPU brand:Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
> > Build CPU family:   6   Model: 79   Stepping: 1
> > Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt
> > lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
> > rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> > C compiler: /usr/bin/cc GNU 4.8.5
> > C compiler flags:-march=core-avx2-Wextra
> > -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall
> > -Wno-unused -Wunused-value -Wunused-parameter  -O3 -DNDEBUG
> > -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds
> > C++ compiler:   /usr/bin/c++ GNU 4.8.5
> > C++ compiler flags:  -march=core-avx2-Wextra
> > -Wno-missing-field-initializers -Wpointer-arith -Wall
> > -Wno-unused-function  -O3 -DNDEBUG -funroll-all-loops
> > -fexcess-precision=fast  -Wno-array-bounds
> > Boost version:  1.53.0 (external)
> > CUDA compiler:  /usr/local/cuda-8.0/bin/nvcc nvcc: NVIDIA (R) Cuda
> > compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on
> > Sun_Sep__4_22:14:01_CDT_2016;Cuda compilation tools, release 8.0, V8.0.44
> > CUDA compiler
> flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=comp
> > ute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-
> > gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_
> > 50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-
> > gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_
> > 61,code=sm_61;-gencode;arch=compute_60,code=compute_60;-
> > gencode;arch=compute_61,code=compute_61;-use_fast_math;;
> > ;-march=core-avx2;-Wextra;-Wno-missing-field-initializers;-
> > Wpointer-arith;-Wall;-Wno-unused-function;-O3;-DNDEBUG;-
> > funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds;
> > CUDA driver:8.0
> > CUDA runtime:   8.0
> >
> >
> > Number of logical cores detected (28) does not match the number reported
> > by OpenMP (1).
> > Consider setting the launch configuration manually!
> >
> > Running on 1 node with total 28 logical cores, 1 compatible GPU
> > Hardware detected on host tiger-i23g14 (the node of MPI rank 0):
> >   CPU info:
> > Vendor: GenuineIntel
> > Brand:  Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
> > Family:  6  model: 79  stepping:  1
> > CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt
> > lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
> > rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> > SIMD instructions most likely to fit this hardware: AVX2_256
> > SIMD instructions selected at GROMACS compile time: AVX2_256
> >   GPU info:
> > Number of GPUs detected: 1

Re: [gmx-users] gromacs-5.1.4 installation issue

[abhisek Mondal]

On Wed, May 24, 2017 at 6:08 PM, Mark Abraham 
wrote:

> Hi,
>
> You should ask the cluster maintainers how they intend the compiler to be
> used. You need to find the same infrastructure at run time as you used at
> compile time, e.g. by loading the same modules.
>
> Yes I did check.
I have 2 cluster with identical configurations. In Cluster_1 it compiled
well and running nicely.
But in Cluster_2 it is giving this error.

To check the GLIBCXX version available in both Clusters, we used: strings
/usr/lib/libstdc++.so.6 | grep GLIBCXX
Output of BOTH clusters:
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_FORCE_NEW
GLIBCXX_DEBUG_MESSAGE_LENGTH

So, I'm confused regarding both the machine does not have  `GLIBCXX_3.4.15`
, then why in one machine /gromacs-5.1.4/lib64/libgromacs_mpi.so.1 is
raising error but not in the other ?

Is there any way to overcome this ? I'm really confused.

Some advice regarding this concern will be highly appreciated.

Thank you.



> Mark
>
> On Wed, May 24, 2017 at 2:13 PM abhisek Mondal 
> wrote:
>
> > Hi,
> >
> >I have been trying to install latest version of gromacs
> (Gromacs-5.1.4)
> > in my cluster.
> >
> > Installation went without any error. But whenever I'm giving the command:
> > gmx_mpi
> > An error report comes:
> > gmx_mpi: /lib64/libz.so.1: no version information available (required by
> > /app/gromacs-5.1.4/lib64/libgromacs_mpi.so.1)
> > gmx_mpi: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found
> > (required by /app/gromacs-5.1.4/lib64/libgromacs_mpi.so.1)
> >
> >
> > Can you please help me out here, regarding what is going wrong here.
> >
> > Thank you.
> >
> > --
> > Abhisek Mondal
> >
> > *Senior Research Fellow*
> >
> > *Structural Biology and Bioinformatics Division*
> > *CSIR-Indian Institute of Chemical Biology*
> >
> > *Kolkata 700032*
> >
> > *INDIA*
> > --
> > 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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> >
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> >
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-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
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[gmx-users] grompp error

[‪Mohammad Roostaie‬ ‪]

Hi GROMACS users,


 
I want to simulate a graphene sheet, and I want to use OPLS-AA force field. So, 
I copied the forcefield in my directory and changed some the files in it 
(ffbonded.itp, ffnonbonded.itp, atomtype.atp, aminoacids.rtp, and 
atomname2type.n2t). I used the pdb2gmx command to create the first topology and 
coordinate files with the modified OPLS-AA forcefield, then I created a box and 
solvated it with water. But, when I wanted to add ions to the box by using “gmx 
grompp -f ions.mdp -c gr_solv.gro -p gr.top -o ions.tpr”, I got this error: 


NOTE 1 [file ions.mdp]:  With Verlet lists the optimal nstlist is >= 10, with 
GPUs >= 20. Note  that with the Verlet scheme, nstlist has no effect on the 
accuracy of  your simulation.
Setting the LD random seed to 209904318
WARNING 1 [file ffbonded.itp, line 305]:  Overriding Bond parameters.
  old:                                          0.151 292880 0.151 292880  new: 
C     C       1    0.14000   392459.2
Generated 36 of the 36 non-bonded parameter combinationsGenerating 1-4 
interactions: fudge = 0.5Generated 36 of the 36 1-4 parameter 
combinations
---Program gmx grompp, 
VERSION 5.1.4Source code file: 
/home/jemmyhu/work/software/gromacs/gromacs-5.1.4/src/gromacs/gmxpreprocess/topio.c,
 line: 755
Fatal error:Syntax error - File forcefield.itp, line 18Last line read:'[ 
defaults ]'Invalid order for directive defaultsFor more information and tips 
for troubleshooting, please check the GROMACSwebsite at 
http://www.gromacs.org/Documentation/Errors

Can you please help me to solve this problem?
Thanks,Mohammad
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