[gmx-users] Free Energy Calculations: Error during minimization step.

[Abhishek Acharya]

Dear GROMACS users,

I am trying to estimate the free energy of solvation for a ion. But, I am
facing a problem while running simulations for the deltaG_LJ calculation.
The simulation at vdw_lambda=1.0 crashes during the steepest-descent
minimization step, with the following error.

---
Program gmx mdrun, VERSION 5.1.2
Source code file:
/home/bp-lab/Downloads/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555

Fatal error:

step 10: Water molecule starting at atom 120 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

The free energy parameters I used for this run are as follows:
*
free_energy  = yes
couple-moltype   = Protein
couple-lambda0   = vdw
couple-lambda1   = none
couple-intramol  = no
init-lambda  = -1
init_lambda_state= 20
delta_lambda = 0
nstdhdl  = 10
fep-lambdas  =
mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
vdw_lambdas  = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
bonded_lambdas   = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
temperature_lambdas  = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
calc_lambda_neighbors= 1
init-lambda-weights  =
dhdl-print-energy= no
sc-alpha = 0.5
sc-power = 1
sc-r-power   = 6
sc-sigma = 0.3
sc-coul  = no
separate-dhdl-file   = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_spacing  = 0.1
*

Out of curiosity, I also ran simulations for a reverse transformation with
the following parameters (and I hope they are correct):

*
free_energy  = yes
couple-moltype   = Protein
couple-lambda0   = none
couple-lambda1   = vdw
couple-intramol  = no
init-lambda  = -1
init_lambda_state= 0
delta_lambda = 0
nstdhdl  = 10
fep-lambdas  =
mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
vdw_lambdas  = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
bonded_lambdas   = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
temperature_lambdas  = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
calc_lambda_neighbors= 1
init-lambda-weights  =
dhdl-print-energy= no
sc-alpha = 0.5
sc-power = 1
sc-r-power   = 6
sc-sigma = 0.3
sc-coul  = no
separate-dhdl-file   = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_spacing  = 0.1
*
Intriguingly, I this case I got the exact error as above, but this time at
lambda=0.
---
Program gmx mdrun, VERSION 5.1.2
Source code file:
/home/bp-lab/Downloads/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555

Fatal error:

step 10: Water molecule starting at atom 120 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

[gmx-users] Protein break after simulation

[ISHRAT JAHAN]

Dear all,
I have done 100ns md simulation of protein with drug using amber99sb.ff
with gromacs-5.1.4 version. After simulation i found my protein broken into
smaller parts in .gro file but when i load the final xtc file to pr.gro
molecule does not break. I have applied -pbc nojump ,cluster and whole but
unable to solve the problem.
Will anyone help me to solve the above problem.
Thanks in advance
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Re: [gmx-users] GPU-accelerated EM

[Alex]

Mark,

I agree with you 100%, given how I've always used particle-based simulation
tools. It is my understanding that my colleague is optimizing custom
forcefields based on EM, followed by short MD. The work is also unrelated
to what most of the GMX community does, so I stay away from this part.
What happens then is also perception-dependent. On our older boxes without
GPU acceleration, he'd see equally sluggish performance from EM and MD,
while now his EM (when submitted incorrectly) runs slowly and the MD
portion completes in a quick burst. This can be perceived as EM being the
bottleneck. Before my initial post, we already decided on CPU-only EM and
your advice to move the EM portion elsewhere (e.g. our old machines) is
even better.

Thanks,

Alex


On Fri, Sep 8, 2017 at 4:27 PM, Mark Abraham 
wrote:

> Hi,
>
> The em log files report using the GPUs, and they do. It just isn't very
> useful because the EM implementations do a lot more neighbour search
> stages, which doesn't use the GPUs.
>
> So, if there's other work for the GPUs to do, then I would plan to run a
> workflow heavily dominated by EM, on a non-GPU resource.
>
> We're not aware of a use case that would justify thinking about how to make
> a correct implementation of EM that could do less searching, because in
> most cases the time spent in EM is a tiny fraction of the time spent in MD.
> Is the workflow useful to optimize in this way?
>
> Mark
>
> On Fri, Sep 8, 2017 at 11:53 PM Alex  wrote:
>
> > Hi all,
> >
> > I tend to run one fat node-wise simulation, but we have another user
> whose
> > use case is different. He runs a bunch of small jobs at the same time and
> > in his case most of the time is taken up by the EM. We have two
> > hyperthreaded Xeons E5 (44 cores total) and 3 GPUs.
> >
> > So, we try to run 10 jobs using 4 cores each. Each mdrun line includes
> >
> > -ntomp 4 -pin on -pinoffset x -pinstride 1 -gpu_id y
> >
> > where pinoffset is 0, 4, 8, etc for the first, second, etc, simulation
> and
> > y changes from 0 to 2 so that the first two GPUs are subscribed three
> > times, while the third one is subscribed four times.
> >
> > Upon submitting this batch, each mdrun instance utilizes something like
> 10%
> > of CPU and the EM jobs proceed slowly. Removing GPU and setting -nb cpu
> > seems to fix that. With MD, everything works properly, but with EM
> there's
> > no GPU acceleration and low CPU usage. Is this correct behavior?
> >
> > Thanks,
> >
> > Alex
> > --
> > 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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Re: [gmx-users] Running multiple Gromacs simulations on the same node

[Mark Abraham]

Hi,

On Sat, Sep 9, 2017 at 12:23 AM MING HA 
wrote:

> Hi all,
>
>
> Thanks for getting back to me so quickly. I found that when I did not
> specify any
> pinning, the running time of each simulation on the same node scaled
> proportionally
> to the number of concurrent Gromacs simulations. After some testing, i
> found that
> when I do not pin the core on which the simulations runs, then each Gromacs
> simulations get mapped to the same process.
>

That's up to your OS. If you check your log files, you will see comments
from mdrun about what it noticed about the pinning context. Obviously, if
it detects something else pinning threads, it respects that.



> I have two questions:
> 1) Is the core on which the simulation runs pre-defined (e.g. each gromacs
> simulation
> starts on Core 0)?
>

That depends exactly how you were running GROMACS, which we don't know.
Other infrastructure like OS, HPC job schedulers, and MPI libraries tend to
get involved here, too...

2) Is there a way to tell Gromacs to allow the OS of the machine to
> automatically schedule
> different processes to run on different cores?
>

mdrun can be instructed to control everything, see the examples in
http://manual.gromacs.org/documentation/2016.3/user-guide/mdrun-performance.html#examples-for-mdrun-on-one-node.
To handle this use case, you need to use either the mdrun options, or some
external tool to handle all these details explicitly, because there is no
way for mdrun to understand that there are other mdrun processes and how it
should manage that.

Mark


> Thanks,
> Ming
>
> On Fri, Sep 8, 2017 at 9:07 AM, Szilárd Páll 
> wrote:
>
> > If you run MPI-enabled GROMACS and start N simulation with M(=1) ranks
> > each, you will have N*M processes. That's how MPI works. However, you
> > do not necessarily need to use MPI; the default build uses thread-MPI,
> > for instance.
> >
> > --
> > Szilárd
> >
> > On Fri, Sep 8, 2017 at 6:00 AM, MING HA  >
> > wrote:
> > > Hi all,
> > >
> > >
> > > It may seem a bit weird, but I'm trying to run multiple Gromacs
> > simulations
> > > simultaneously on the same node, and I specified each Gromacs
> simulation
> > > to use only 1 MPI process and 1 OMP thread. I'm doing this because I am
> > > trying to check how accurate my model can predict an application using
> a
> > > single thread and process.
> > >
> > > My question is: If, for example, I am running multiple Gromacs
> > simulations
> > > simultaneously, each with 1 MPI process and 1 OMP thread,  on the same
> > > node, does each simulation use separate MPI processes and OMP threads,
> > > or are they shared?
> > >
> > >
> > > Sincerely,
> > > Ming
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
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> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> > --
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> >
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Re: [gmx-users] GPU-accelerated EM

[Mark Abraham]

Hi,

The em log files report using the GPUs, and they do. It just isn't very
useful because the EM implementations do a lot more neighbour search
stages, which doesn't use the GPUs.

So, if there's other work for the GPUs to do, then I would plan to run a
workflow heavily dominated by EM, on a non-GPU resource.

We're not aware of a use case that would justify thinking about how to make
a correct implementation of EM that could do less searching, because in
most cases the time spent in EM is a tiny fraction of the time spent in MD.
Is the workflow useful to optimize in this way?

Mark

On Fri, Sep 8, 2017 at 11:53 PM Alex  wrote:

> Hi all,
>
> I tend to run one fat node-wise simulation, but we have another user whose
> use case is different. He runs a bunch of small jobs at the same time and
> in his case most of the time is taken up by the EM. We have two
> hyperthreaded Xeons E5 (44 cores total) and 3 GPUs.
>
> So, we try to run 10 jobs using 4 cores each. Each mdrun line includes
>
> -ntomp 4 -pin on -pinoffset x -pinstride 1 -gpu_id y
>
> where pinoffset is 0, 4, 8, etc for the first, second, etc, simulation and
> y changes from 0 to 2 so that the first two GPUs are subscribed three
> times, while the third one is subscribed four times.
>
> Upon submitting this batch, each mdrun instance utilizes something like 10%
> of CPU and the EM jobs proceed slowly. Removing GPU and setting -nb cpu
> seems to fix that. With MD, everything works properly, but with EM there's
> no GPU acceleration and low CPU usage. Is this correct behavior?
>
> Thanks,
>
> Alex
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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Re: [gmx-users] Running multiple Gromacs simulations on the same node

[MING HA]

Hi all,


Thanks for getting back to me so quickly. I found that when I did not
specify any
pinning, the running time of each simulation on the same node scaled
proportionally
to the number of concurrent Gromacs simulations. After some testing, i
found that
when I do not pin the core on which the simulations runs, then each Gromacs
simulations get mapped to the same process.

I have two questions:
1) Is the core on which the simulation runs pre-defined (e.g. each gromacs
simulation
starts on Core 0)?

2) Is there a way to tell Gromacs to allow the OS of the machine to
automatically schedule
different processes to run on different cores?


Thanks,
Ming

On Fri, Sep 8, 2017 at 9:07 AM, Szilárd Páll  wrote:

> If you run MPI-enabled GROMACS and start N simulation with M(=1) ranks
> each, you will have N*M processes. That's how MPI works. However, you
> do not necessarily need to use MPI; the default build uses thread-MPI,
> for instance.
>
> --
> Szilárd
>
> On Fri, Sep 8, 2017 at 6:00 AM, MING HA 
> wrote:
> > Hi all,
> >
> >
> > It may seem a bit weird, but I'm trying to run multiple Gromacs
> simulations
> > simultaneously on the same node, and I specified each Gromacs simulation
> > to use only 1 MPI process and 1 OMP thread. I'm doing this because I am
> > trying to check how accurate my model can predict an application using a
> > single thread and process.
> >
> > My question is: If, for example, I am running multiple Gromacs
> simulations
> > simultaneously, each with 1 MPI process and 1 OMP thread,  on the same
> > node, does each simulation use separate MPI processes and OMP threads,
> > or are they shared?
> >
> >
> > Sincerely,
> > Ming
> > --
> > 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
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> send a mail to gmx-users-requ...@gromacs.org.
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[gmx-users] GPU-accelerated EM

[Alex]

Hi all,

I tend to run one fat node-wise simulation, but we have another user whose
use case is different. He runs a bunch of small jobs at the same time and
in his case most of the time is taken up by the EM. We have two
hyperthreaded Xeons E5 (44 cores total) and 3 GPUs.

So, we try to run 10 jobs using 4 cores each. Each mdrun line includes

-ntomp 4 -pin on -pinoffset x -pinstride 1 -gpu_id y

where pinoffset is 0, 4, 8, etc for the first, second, etc, simulation and
y changes from 0 to 2 so that the first two GPUs are subscribed three
times, while the third one is subscribed four times.

Upon submitting this batch, each mdrun instance utilizes something like 10%
of CPU and the EM jobs proceed slowly. Removing GPU and setting -nb cpu
seems to fix that. With MD, everything works properly, but with EM there's
no GPU acceleration and low CPU usage. Is this correct behavior?

Thanks,

Alex
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Re: [gmx-users] Gromacs 2016.3 MPI Message truncated error

[Mark Abraham]

Hi,

That error doesn't come from GROMACS, so I can only suspect some kind of
misconfiguration or transient error with your MPI system.

Mark

On Fri, Sep 8, 2017 at 4:15 PM Farkas-Pall, Kristof <
kristof.farkas-pall...@ucl.ac.uk> wrote:

> Hello,
>
> Trying to run a simulation on 1 node 32 cores (Cray XE6).
>
> After running for a number of steps, the code exits with error described
> below.
>
> In my submission script I have:
>
> ```
> #PBS -l nodes=1:ppn:32:xe
>
> aprun -n 32 gmx_mpi mdrun -deffnm replica_0/lambda_0/minimize
> ```
>
> All info is coming from mdrun:
>
> ```
> GROMACS:  gmx mdrun, version 2016.3
> Executable: xxx/gromacs/gromacs-2016.3/install-cpu/bin/gmx_mpi
>
> Running on 1 node with total 32 cores, 32 logical cores
> Hardware detected on host nidX (the node of MPI rank 0):
>   CPU info:
> Vendor: AMD
> Brand:  AMD Opteron(TM) Processor 6276
> SIMD instructions most likely to fit this hardware: AVX_128_FMA
> SIMD instructions selected at GROMACS compile time: AVX_128_FMA
>
>   Hardware topology: Basic
>
> The number of OpenMP threads was set by environment variable
> OMP_NUM_THREADS to 1
>
> Will use 20 particle-particle and 12 PME only ranks
> This is a guess, check the performance at the end of the log file
> Using 32 MPI processes
> Using 1 OpenMP thread per MPI process
>
>
> Non-default thread affinity set probably by the OpenMP library,
> disabling internal thread affinity
>
> Rank 19 [Thu Sep  7 14:04:02 2017] [c23-1c0s7n3] Fatal error in
> MPI_Sendrecv: Message truncated, error stack:
> MPI_Sendrecv(249).: MPI_Sendrecv(sbuf=0x7fff3f90,
> scount=8, MPI_BYTE, dest=17, stag=0, rbuf=0x7fff4060, rcount=8,
> MPI_BYTE, src=7, rtag=0, comm=0x8402, status=0x7fff3e70) failed
> MPIDI_CH3U_Receive_data_found(144): Message from rank 7 and tag 0
> truncated; 264 bytes received but buffer size is 8
> _pmiu_daemon(SIGCHLD): [NID 14929] [c23-1c0s7n3] [Thu Sep  7 14:04:02
> 2017] PE RANK 19 exit signal Aborted
>
> ```
>
> Is this because Gromacs wasn't built correctly? Or setting the aprun
> variables incorrectly?
>
> Thanks for any help!
>
> Kristof
>
>
>
>
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Re: [gmx-users] Result analysis of protein water

[Deep kumar]

Thanks Smith,



On Fri, Sep 8, 2017 at 7:38 PM, Smith, Micholas D.  wrote:

> First: Welcome to the wonderful world of MD.
>
> Second, 10ns for a 164 residue protein is nowhere near enough simulation
> time. If you are looking for just small modifications, you could do an
> alignment of the backbones of the proteins in each trajectory and compare
> all frames to all-frames using the rmsd (you'd end up with a matrix of rmsd
> values comparing trajectory 1 to trajectory 2).
>

I am looking to perform conformational (such as if due to mutation protein
unfolds) and free energy change after the mutation. Please let me know what
kind of analysis should be done for such an aim. And, please share how many
ns MD is apt for 164 residues or more.

>
> Other things to consider are: salt-bridges, hydrogen-bond networks, and
> secondary-structure measurements (STRIDE or DSSP).
>

Could you please share more details on how these analysis can be performed?


Thanks much!


>
> Good Luck.
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Deep
> kumar 
> Sent: Friday, September 08, 2017 12:30 PM
> To: gromacs.org_gmx-users@maillist.sys.kth.se; gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Result analysis of protein water
>
> Hello All,
>
> I have performed MD on a protein water for 10ns, protein with total 164
> residues in two chains. I have got the result graphs of radius of gyration
> and rmsd for both wild and mutant. Wanted to attach the graphs but could
> not due to bytes limit. There is one residue mutation (M -> T) in the
> protein. I am new to MD analysis. Could you please let me know how to know
> if the mutation is causing any conformational change. I can look at the
> trajectories obtained of wild and mutant type, but to make accurate
> analysis I would need more information. Also, please do share with me how
> can i do more analysis to see the effect of mutations. Please let me know
> if I need to provide more information.
>
> Thanks & Regards.
> --
> 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] easy sampling of data

[Nikhil Maroli]

http://manual.gromacs.org/programs/gmx-trjconv.html
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[gmx-users] easy sampling of data

[gangotri dey]

Dear all,

I have a simulation that I ran for 5 ns. I have saved after every 0.1 ps. I
would like to extract the structure after every 1 ns.  Is there any easy
way to do it in gromacs?


*Thank you*

*Gangotri Dey*
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Re: [gmx-users] Result analysis of protein water

[Smith, Micholas D.]

First: Welcome to the wonderful world of MD. 

Second, 10ns for a 164 residue protein is nowhere near enough simulation time. 
If you are looking for just small modifications, you could do an alignment of 
the backbones of the proteins in each trajectory and compare all frames to 
all-frames using the rmsd (you'd end up with a matrix of rmsd values comparing 
trajectory 1 to trajectory 2). 

Other things to consider are: salt-bridges, hydrogen-bond networks, and 
secondary-structure measurements (STRIDE or DSSP).

Good Luck.

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Deep kumar 

Sent: Friday, September 08, 2017 12:30 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se; gmx-us...@gromacs.org
Subject: Re: [gmx-users] Result analysis of protein water

Hello All,

I have performed MD on a protein water for 10ns, protein with total 164
residues in two chains. I have got the result graphs of radius of gyration
and rmsd for both wild and mutant. Wanted to attach the graphs but could
not due to bytes limit. There is one residue mutation (M -> T) in the
protein. I am new to MD analysis. Could you please let me know how to know
if the mutation is causing any conformational change. I can look at the
trajectories obtained of wild and mutant type, but to make accurate
analysis I would need more information. Also, please do share with me how
can i do more analysis to see the effect of mutations. Please let me know
if I need to provide more information.

Thanks & Regards.
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Re: [gmx-users] Result analysis of protein water

[Deep kumar]

Hello All,

I have performed MD on a protein water for 10ns, protein with total 164
residues in two chains. I have got the result graphs of radius of gyration
and rmsd for both wild and mutant. Wanted to attach the graphs but could
not due to bytes limit. There is one residue mutation (M -> T) in the
protein. I am new to MD analysis. Could you please let me know how to know
if the mutation is causing any conformational change. I can look at the
trajectories obtained of wild and mutant type, but to make accurate
analysis I would need more information. Also, please do share with me how
can i do more analysis to see the effect of mutations. Please let me know
if I need to provide more information.

Thanks & Regards.
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[gmx-users] umbrella sampling

[Nivedita Rai]

Dear gromacs developers,

I am trying to implement umbrella sampling in my work but instead of
distance pulling i want to do rotational pull with the gap of 10 degree. I
went through your tutorial and many articles but im unable to find  how to
implement rotational pull in .mdp file. will you please guide me or send me
any article which i can refer for my objective.


-- 
Thanks and regards


Nivedita Rai
PhD in Bioinformatics
Centre for Bioinformatics
Pondicherry University, Pondicherry (605014), INDIA
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Re: [gmx-users] trjconv -fit progressive

[edesantis]

thanks Justin for your quick responce

have a nice weekend
Emiliano


On 2017-09-08 17:59, Justin Lemkul wrote:

On 9/8/17 11:57 AM, edesantis wrote:

Hi gromacs users,

I removed the boundary effects on my system box during the trajectory 
of protein crystal simulation following the Suggested trjconv workflow


http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions 
then I need to fit the trj to remove rotations and translations (my 
propose is to reproduce a scattering pattern of the crystal, so I want 
that all frames are superimposable)


so I tough to use -fit rot+trans

looking at the trjconv manual I've seen also the flag -fit 
progressive,

but actually I didn't understand what does this operation do,
do you know it?



It's described in the help info:

"There are two options for fitting the trajectory to a reference either 
for
essential dynamics analysis, etc. The first option is just plain 
fitting to a
reference structure in the structure file. The second option is a 
progressive
fit in which the first timeframe is fitted to the reference structure 
in the

structure file to obtain and each subsequent timeframe is fitted to the
previously fitted structure. This way a continuous trajectory is 
generated,
which might not be the case when using the regular fit method, e.g. 
when your

protein undergoes large conformational transitions."

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==


--
Emiliano De Santis
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Re: [gmx-users] trjconv -fit progressive

[Justin Lemkul]

On 9/8/17 11:57 AM, edesantis wrote:

Hi gromacs users,

I removed the boundary effects on my system box during the trajectory 
of protein crystal simulation following the Suggested trjconv workflow


http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions 




then I need to fit the trj to remove rotations and translations (my 
propose is to reproduce a scattering pattern of the crystal, so I want 
that all frames are superimposable)


so I tough to use -fit rot+trans

looking at the trjconv manual I've seen also the flag -fit progressive,
but actually I didn't understand what does this operation do,
do you know it?



It's described in the help info:

"There are two options for fitting the trajectory to a reference either for
essential dynamics analysis, etc. The first option is just plain fitting 
to a
reference structure in the structure file. The second option is a 
progressive

fit in which the first timeframe is fitted to the reference structure in the
structure file to obtain and each subsequent timeframe is fitted to the
previously fitted structure. This way a continuous trajectory is generated,
which might not be the case when using the regular fit method, e.g. when 
your

protein undergoes large conformational transitions."

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] trjconv -fit progressive

[edesantis]

Hi gromacs users,

I removed the boundary effects on my system box during the trajectory of 
protein crystal simulation following the Suggested trjconv workflow


http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


then I need to fit the trj to remove rotations and translations (my 
propose is to reproduce a scattering pattern of the crystal, so I want 
that all frames are superimposable)


so I tough to use -fit rot+trans

looking at the trjconv manual I've seen also the flag -fit progressive,
but actually I didn't understand what does this operation do,
do you know it?


thank you in advance for your help,

bye
Emiliano
--
Emiliano De Santis
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Re: [gmx-users] Merging different topology files

[Justin Lemkul]

On 9/8/17 10:19 AM, Momin Ahmad wrote:

Hi Justin,

could you provide me a link to some tutorials that focus more on the 
program structure than on the results of simulations? I did some 
protein simulation tutorials that did not really help me in 
understanding the software itself. Big thanks in advance.




I'll recommend my own:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html

I have a couple examples of analysis, but I purposefully do not 
emphasize analysis/outcomes in my tutorials.  This one has lots of 
detail about what every program is doing, what the options mean, and 
what the structure of the topology is.  Beyond that, for learning about 
topologies, Chapter 5 of the manual is your best resource, as is Google 
(every problem you might encounter has been solved at least once before, 
I'm fairly sure).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] trjconv not able to generated output

[Sergio Manzetti]

Sorry, my mistake. You better put me away with Zuckerberg and those guys. 

Have a good weekend! 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Friday, September 8, 2017 4:16:57 PM 
Subject: Re: [gmx-users] trjconv not able to generated output 

On 9/8/17 9:47 AM, Sergio Manzetti wrote: 
> I have done this many times before, its doesn't give any problems, it gives 
> the last frame and only that. But not in this case 

What do you mean? The screen output says it wrote a coordinate file at 
t=2000 ps. 

-Justin 

> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | 
> FAP ] 
> 
> 
> 
> From: "Justin Lemkul"  
> To: "gmx-users"  
> Sent: Friday, September 8, 2017 3:52:52 PM 
> Subject: Re: [gmx-users] trjconv not able to generated output 
> 
> On 9/8/17 9:38 AM, Sergio Manzetti wrote: 
>> Hi, I have tried several ways to get the last frame from the output xtc 
>> using gmx trjconv, like: 
>> 
>> sem@Fjordforsk:/media/sem/HDD3/files/sims/BPRP/5$ gmx trjconv -f traj_c -o 
>> confout.gro -b 2000 -e 2000 
>> :-) GROMACS - gmx trjconv, VERSION 5.1.2 (-: 
>> 
>> GROMACS is written by: 
>> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar 
>> Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch 
>> Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen 
>> Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner 
>> Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff 
>> Erik Marklund Teemu Murtola Szilard Pall Sander Pronk 
>> Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers 
>> Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf 
>> and the project leaders: 
>> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel 
>> 
>> Copyright (c) 1991-2000, University of Groningen, The Netherlands. 
>> Copyright (c) 2001-2015, The GROMACS development team at 
>> Uppsala University, Stockholm University and 
>> the Royal Institute of Technology, Sweden. 
>> check out http://www.gromacs.org for more information. 
>> 
>> GROMACS is free software; you can redistribute it and/or modify it 
>> under the terms of the GNU Lesser General Public License 
>> as published by the Free Software Foundation; either version 2.1 
>> of the License, or (at your option) any later version. 
>> 
>> GROMACS: gmx trjconv, VERSION 5.1.2 
>> Executable: /usr/bin/gmx 
>> Data prefix: /usr 
>> Command line: 
>> gmx trjconv -f traj_c -o confout.gro -b 2000 -e 2000 
>> 
>> Will write gro: Coordinate file in Gromos-87 format 
>> Reading file topol.tpr, VERSION 5.1.2 (single precision) 
>> Reading file topol.tpr, VERSION 5.1.2 (single precision) 
>> Select group for output 
>> Group 0 ( System) has 50510 elements 
>> Group 1 ( DNA) has 1333 elements 
>> Group 2 ( NA) has 71 elements 
>> Group 3 ( CL) has 31 elements 
>> Group 4 ( PRB) has 28 elements 
>> Group 5 ( Ion) has 102 elements 
>> Group 6 ( NA) has 71 elements 
>> Group 7 ( CL) has 31 elements 
>> Group 8 ( PRB) has 28 elements 
>> Group 9 ( Other) has 28 elements 
>> Group 10 ( NA) has 71 elements 
>> Group 11 ( CL) has 31 elements 
>> Group 12 ( PRB) has 28 elements 
>> Group 13 ( Water) has 49047 elements 
>> Group 14 ( SOL) has 49047 elements 
>> Group 15 ( non-Water) has 1463 elements 
>> Group 16 ( Water_and_ions) has 49149 elements 
>> Select a group: 15 
>> Selected 15: 'non-Water' 
>> Reading frame 0 time 2000.000 
>> Precision of traj_c.xtc is 0.001 (nm) 
>> Using output precision of 0.001 (nm) 
>> 
>> Back Off! I just backed up confout.gro to ./#confout.gro.1# 
>> Last frame 0 time 2000.000 
>> 
>> however, something is wrong with the trajectory, even tried the xtc, same 
>> problem there. There seems to be enough frames, but they don't "appear" 
>> after the selection of groups. 
> You're telling trjconv to skip everything before 2000 ps with -b 2000, 
> so the program will not report any reading of frames before that time. 
> If there was actually a problem, the program would crash with a fatal error. 
> 
>> How can I repair or check a trajectory? 
> gmx check, and it will surely report that everything is fine. 
> 
> -Justin 
> 

-- 
== 

Justin A. Lemkul, Ph.D. 
Assistant Professor 
Virginia Tech Department of Biochemistry 

303 Engel Hall 
340 West Campus Dr.

Re: [gmx-users] Merging different topology files

[Momin Ahmad]

Hi Justin,

could you provide me a link to some tutorials that focus more on the 
program structure than on the results of simulations? I did some protein 
simulation tutorials that did not really help me in understanding the 
software itself. Big thanks in advance.


Cheers,
Momin

Am 08.09.2017 um 13:42 schrieb Justin Lemkul:



On 9/8/17 5:50 AM, Momin Ahmad wrote:
Thank you for your help. I already did that but i get a weird error 
that i can not solve. I attached the topology files and the error 
message. Maybe the numbering of the residues has to be changed? 
Thanks in advance.




You have lots of missing parameters, which means your force field 
doesn't know how to represent these molecules.  You are also missing 
several bonded interactions in your ammonia topology, so the 
simulation won't be stable.  As to the last fatal error, your 
[molecules] directive doesn't actually specify how many molecules you 
have:


[molecules]
AMMONIA
METHANE

There need to be actual numbers here.  Please go back and do some 
basic GROMACS tutorials and reading in the PDF manual (particularly 
Chapter 5) to understand topology format before trying to do something 
like this.  It's very easy to make lots of mistakes, some obvious and 
some not.


-Justin


Cheers,

Momin


Am 07.09.2017 um 21:08 schrieb Justin Lemkul:



On 9/7/17 10:19 AM, Momin Ahmad wrote:

Hello all,

is there a simple way to merge two or more topology files into one? 
I am trying to use grompp to set up a simulation but my solvation 
contains different molecules which have different .top files. I 
also tried creating a main topology file which includes the other 
two topologies but without success. Hope anyone knows how to solve 
this.




The #include mechanism is the only way to do this.  If you have two 
.top (system topology) files, then:


1. Remove any #include statement for a parent force field (i.e. the 
file with [defaults] in it)

2. Remove any [system] or [molecules] directive

(you now have proper .itp format)

3. Remove any redundant #include statements (e.g. for water, ions) 
to avoid "moleculetype redefined" errors
4. Construct a new .top that #includes a parent force field, your 
two new .itp files, and has [system] and [molecules] directives.


-Justin









--
Momin Ahmad

Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Phone: +49 721 608-24286
E-Mail: momin.ah...@kit.edu

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Re: [gmx-users] trjconv not able to generated output

[Justin Lemkul]

On 9/8/17 9:47 AM, Sergio Manzetti wrote:

I have done this many times before, its doesn't give any problems, it gives the 
last frame and only that. But not in this case


What do you mean?  The screen output says it wrote a coordinate file at 
t=2000 ps.


-Justin



Sergio Manzetti

[ http://www.fjordforsk.no/logo_hr2.jpg ]

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ]



From: "Justin Lemkul" 
To: "gmx-users" 
Sent: Friday, September 8, 2017 3:52:52 PM
Subject: Re: [gmx-users] trjconv not able to generated output

On 9/8/17 9:38 AM, Sergio Manzetti wrote:

Hi, I have tried several ways to get the last frame from the output xtc using 
gmx trjconv, like:

sem@Fjordforsk:/media/sem/HDD3/files/sims/BPRP/5$ gmx trjconv -f traj_c -o 
confout.gro -b 2000 -e 2000
:-) GROMACS - gmx trjconv, VERSION 5.1.2 (-:

GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS: gmx trjconv, VERSION 5.1.2
Executable: /usr/bin/gmx
Data prefix: /usr
Command line:
gmx trjconv -f traj_c -o confout.gro -b 2000 -e 2000

Will write gro: Coordinate file in Gromos-87 format
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Select group for output
Group 0 ( System) has 50510 elements
Group 1 ( DNA) has 1333 elements
Group 2 ( NA) has 71 elements
Group 3 ( CL) has 31 elements
Group 4 ( PRB) has 28 elements
Group 5 ( Ion) has 102 elements
Group 6 ( NA) has 71 elements
Group 7 ( CL) has 31 elements
Group 8 ( PRB) has 28 elements
Group 9 ( Other) has 28 elements
Group 10 ( NA) has 71 elements
Group 11 ( CL) has 31 elements
Group 12 ( PRB) has 28 elements
Group 13 ( Water) has 49047 elements
Group 14 ( SOL) has 49047 elements
Group 15 ( non-Water) has 1463 elements
Group 16 ( Water_and_ions) has 49149 elements
Select a group: 15
Selected 15: 'non-Water'
Reading frame 0 time 2000.000
Precision of traj_c.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)

Back Off! I just backed up confout.gro to ./#confout.gro.1#
Last frame 0 time 2000.000

however, something is wrong with the trajectory, even tried the xtc, same problem there. 
There seems to be enough frames, but they don't "appear" after the selection of 
groups.

You're telling trjconv to skip everything before 2000 ps with -b 2000,
so the program will not report any reading of frames before that time.
If there was actually a problem, the program would crash with a fatal error.


How can I repair or check a trajectory?

gmx check, and it will surely report that everything is fine.

-Justin



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] Gromacs 2016.3 MPI Message truncated error

[Farkas-Pall, Kristof]

Hello,

Trying to run a simulation on 1 node 32 cores (Cray XE6).

After running for a number of steps, the code exits with error described below.

In my submission script I have:

```
#PBS -l nodes=1:ppn:32:xe

aprun -n 32 gmx_mpi mdrun -deffnm replica_0/lambda_0/minimize
```

All info is coming from mdrun:

```
GROMACS:  gmx mdrun, version 2016.3
Executable: xxx/gromacs/gromacs-2016.3/install-cpu/bin/gmx_mpi

Running on 1 node with total 32 cores, 32 logical cores
Hardware detected on host nidX (the node of MPI rank 0):
  CPU info:
Vendor: AMD
Brand:  AMD Opteron(TM) Processor 6276
SIMD instructions most likely to fit this hardware: AVX_128_FMA
SIMD instructions selected at GROMACS compile time: AVX_128_FMA

  Hardware topology: Basic

The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 
1

Will use 20 particle-particle and 12 PME only ranks
This is a guess, check the performance at the end of the log file
Using 32 MPI processes
Using 1 OpenMP thread per MPI process


Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity

Rank 19 [Thu Sep  7 14:04:02 2017] [c23-1c0s7n3] Fatal error in MPI_Sendrecv: 
Message truncated, error stack:
MPI_Sendrecv(249).: MPI_Sendrecv(sbuf=0x7fff3f90, scount=8, 
MPI_BYTE, dest=17, stag=0, rbuf=0x7fff4060, rcount=8, MPI_BYTE, src=7, 
rtag=0, comm=0x8402, status=0x7fff3e70) failed
MPIDI_CH3U_Receive_data_found(144): Message from rank 7 and tag 0 truncated; 
264 bytes received but buffer size is 8
_pmiu_daemon(SIGCHLD): [NID 14929] [c23-1c0s7n3] [Thu Sep  7 14:04:02 2017] PE 
RANK 19 exit signal Aborted

```

Is this because Gromacs wasn't built correctly? Or setting the aprun variables 
incorrectly?

Thanks for any help!

Kristof




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Re: [gmx-users] trjconv not able to generated output

[Sergio Manzetti]

I have done this many times before, its doesn't give any problems, it gives the 
last frame and only that. But not in this case 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Friday, September 8, 2017 3:52:52 PM 
Subject: Re: [gmx-users] trjconv not able to generated output 

On 9/8/17 9:38 AM, Sergio Manzetti wrote: 
> Hi, I have tried several ways to get the last frame from the output xtc using 
> gmx trjconv, like: 
> 
> sem@Fjordforsk:/media/sem/HDD3/files/sims/BPRP/5$ gmx trjconv -f traj_c -o 
> confout.gro -b 2000 -e 2000 
> :-) GROMACS - gmx trjconv, VERSION 5.1.2 (-: 
> 
> GROMACS is written by: 
> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar 
> Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch 
> Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen 
> Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner 
> Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff 
> Erik Marklund Teemu Murtola Szilard Pall Sander Pronk 
> Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers 
> Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf 
> and the project leaders: 
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel 
> 
> Copyright (c) 1991-2000, University of Groningen, The Netherlands. 
> Copyright (c) 2001-2015, The GROMACS development team at 
> Uppsala University, Stockholm University and 
> the Royal Institute of Technology, Sweden. 
> check out http://www.gromacs.org for more information. 
> 
> GROMACS is free software; you can redistribute it and/or modify it 
> under the terms of the GNU Lesser General Public License 
> as published by the Free Software Foundation; either version 2.1 
> of the License, or (at your option) any later version. 
> 
> GROMACS: gmx trjconv, VERSION 5.1.2 
> Executable: /usr/bin/gmx 
> Data prefix: /usr 
> Command line: 
> gmx trjconv -f traj_c -o confout.gro -b 2000 -e 2000 
> 
> Will write gro: Coordinate file in Gromos-87 format 
> Reading file topol.tpr, VERSION 5.1.2 (single precision) 
> Reading file topol.tpr, VERSION 5.1.2 (single precision) 
> Select group for output 
> Group 0 ( System) has 50510 elements 
> Group 1 ( DNA) has 1333 elements 
> Group 2 ( NA) has 71 elements 
> Group 3 ( CL) has 31 elements 
> Group 4 ( PRB) has 28 elements 
> Group 5 ( Ion) has 102 elements 
> Group 6 ( NA) has 71 elements 
> Group 7 ( CL) has 31 elements 
> Group 8 ( PRB) has 28 elements 
> Group 9 ( Other) has 28 elements 
> Group 10 ( NA) has 71 elements 
> Group 11 ( CL) has 31 elements 
> Group 12 ( PRB) has 28 elements 
> Group 13 ( Water) has 49047 elements 
> Group 14 ( SOL) has 49047 elements 
> Group 15 ( non-Water) has 1463 elements 
> Group 16 ( Water_and_ions) has 49149 elements 
> Select a group: 15 
> Selected 15: 'non-Water' 
> Reading frame 0 time 2000.000 
> Precision of traj_c.xtc is 0.001 (nm) 
> Using output precision of 0.001 (nm) 
> 
> Back Off! I just backed up confout.gro to ./#confout.gro.1# 
> Last frame 0 time 2000.000 
> 
> however, something is wrong with the trajectory, even tried the xtc, same 
> problem there. There seems to be enough frames, but they don't "appear" after 
> the selection of groups. 

You're telling trjconv to skip everything before 2000 ps with -b 2000, 
so the program will not report any reading of frames before that time. 
If there was actually a problem, the program would crash with a fatal error. 

> How can I repair or check a trajectory? 

gmx check, and it will surely report that everything is fine. 

-Justin 

-- 
== 

Justin A. Lemkul, Ph.D. 
Assistant Professor 
Virginia Tech Department of Biochemistry 

303 Engel Hall 
340 West Campus Dr. 
Blacksburg, VA 24061 

jalem...@vt.edu | (540) 231-3129 
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html 

== 

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Re: [gmx-users] trjconv not able to generated output

[Justin Lemkul]

On 9/8/17 9:38 AM, Sergio Manzetti wrote:

Hi, I have tried several ways to get the last frame from the output xtc using 
gmx trjconv, like:

sem@Fjordforsk:/media/sem/HDD3/files/sims/BPRP/5$ gmx trjconv -f traj_c -o 
confout.gro -b 2000 -e 2000
:-) GROMACS - gmx trjconv, VERSION 5.1.2 (-:

GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS: gmx trjconv, VERSION 5.1.2
Executable: /usr/bin/gmx
Data prefix: /usr
Command line:
gmx trjconv -f traj_c -o confout.gro -b 2000 -e 2000

Will write gro: Coordinate file in Gromos-87 format
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Reading file topol.tpr, VERSION 5.1.2 (single precision)
Select group for output
Group 0 ( System) has 50510 elements
Group 1 ( DNA) has 1333 elements
Group 2 ( NA) has 71 elements
Group 3 ( CL) has 31 elements
Group 4 ( PRB) has 28 elements
Group 5 ( Ion) has 102 elements
Group 6 ( NA) has 71 elements
Group 7 ( CL) has 31 elements
Group 8 ( PRB) has 28 elements
Group 9 ( Other) has 28 elements
Group 10 ( NA) has 71 elements
Group 11 ( CL) has 31 elements
Group 12 ( PRB) has 28 elements
Group 13 ( Water) has 49047 elements
Group 14 ( SOL) has 49047 elements
Group 15 ( non-Water) has 1463 elements
Group 16 ( Water_and_ions) has 49149 elements
Select a group: 15
Selected 15: 'non-Water'
Reading frame 0 time 2000.000
Precision of traj_c.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)

Back Off! I just backed up confout.gro to ./#confout.gro.1#
Last frame 0 time 2000.000

however, something is wrong with the trajectory, even tried the xtc, same problem there. 
There seems to be enough frames, but they don't "appear" after the selection of 
groups.


You're telling trjconv to skip everything before 2000 ps with -b 2000, 
so the program will not report any reading of frames before that time.  
If there was actually a problem, the program would crash with a fatal error.



How can I repair or check a trajectory?


gmx check, and it will surely report that everything is fine.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] trjconv not able to generated output

[Sergio Manzetti]

Hi, I have tried several ways to get the last frame from the output xtc using 
gmx trjconv, like: 

sem@Fjordforsk:/media/sem/HDD3/files/sims/BPRP/5$ gmx trjconv -f traj_c -o 
confout.gro -b 2000 -e 2000 
:-) GROMACS - gmx trjconv, VERSION 5.1.2 (-: 

GROMACS is written by: 
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar 
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch 
Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen 
Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner 
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff 
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk 
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers 
Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf 
and the project leaders: 
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel 

Copyright (c) 1991-2000, University of Groningen, The Netherlands. 
Copyright (c) 2001-2015, The GROMACS development team at 
Uppsala University, Stockholm University and 
the Royal Institute of Technology, Sweden. 
check out http://www.gromacs.org for more information. 

GROMACS is free software; you can redistribute it and/or modify it 
under the terms of the GNU Lesser General Public License 
as published by the Free Software Foundation; either version 2.1 
of the License, or (at your option) any later version. 

GROMACS: gmx trjconv, VERSION 5.1.2 
Executable: /usr/bin/gmx 
Data prefix: /usr 
Command line: 
gmx trjconv -f traj_c -o confout.gro -b 2000 -e 2000 

Will write gro: Coordinate file in Gromos-87 format 
Reading file topol.tpr, VERSION 5.1.2 (single precision) 
Reading file topol.tpr, VERSION 5.1.2 (single precision) 
Select group for output 
Group 0 ( System) has 50510 elements 
Group 1 ( DNA) has 1333 elements 
Group 2 ( NA) has 71 elements 
Group 3 ( CL) has 31 elements 
Group 4 ( PRB) has 28 elements 
Group 5 ( Ion) has 102 elements 
Group 6 ( NA) has 71 elements 
Group 7 ( CL) has 31 elements 
Group 8 ( PRB) has 28 elements 
Group 9 ( Other) has 28 elements 
Group 10 ( NA) has 71 elements 
Group 11 ( CL) has 31 elements 
Group 12 ( PRB) has 28 elements 
Group 13 ( Water) has 49047 elements 
Group 14 ( SOL) has 49047 elements 
Group 15 ( non-Water) has 1463 elements 
Group 16 ( Water_and_ions) has 49149 elements 
Select a group: 15 
Selected 15: 'non-Water' 
Reading frame 0 time 2000.000 
Precision of traj_c.xtc is 0.001 (nm) 
Using output precision of 0.001 (nm) 

Back Off! I just backed up confout.gro to ./#confout.gro.1# 
Last frame 0 time 2000.000 

however, something is wrong with the trajectory, even tried the xtc, same 
problem there. There seems to be enough frames, but they don't "appear" after 
the selection of groups. 

How can I repair or check a trajectory? 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

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Re: [gmx-users] Running multiple Gromacs simulations on the same node

[Szilárd Páll]

If you run MPI-enabled GROMACS and start N simulation with M(=1) ranks
each, you will have N*M processes. That's how MPI works. However, you
do not necessarily need to use MPI; the default build uses thread-MPI,
for instance.

--
Szilárd

On Fri, Sep 8, 2017 at 6:00 AM, MING HA  wrote:
> Hi all,
>
>
> It may seem a bit weird, but I'm trying to run multiple Gromacs simulations
> simultaneously on the same node, and I specified each Gromacs simulation
> to use only 1 MPI process and 1 OMP thread. I'm doing this because I am
> trying to check how accurate my model can predict an application using a
> single thread and process.
>
> My question is: If, for example, I am running multiple Gromacs simulations
> simultaneously, each with 1 MPI process and 1 OMP thread,  on the same
> node, does each simulation use separate MPI processes and OMP threads,
> or are they shared?
>
>
> Sincerely,
> Ming
> --
> 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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Re: [gmx-users] Running multiple Gromacs simulations on the same node

[Wes Barnett]

On Fri, Sep 8, 2017 at 12:00 AM, MING HA 
wrote:

> Hi all,
>
>
> It may seem a bit weird, but I'm trying to run multiple Gromacs simulations
> simultaneously on the same node, and I specified each Gromacs simulation
> to use only 1 MPI process and 1 OMP thread. I'm doing this because I am
> trying to check how accurate my model can predict an application using a
> single thread and process.
>
> My question is: If, for example, I am running multiple Gromacs simulations
> simultaneously, each with 1 MPI process and 1 OMP thread,  on the same
> node, does each simulation use separate MPI processes and OMP threads,
> or are they shared?
>
>
> Sincerely,
> Ming


I think that depends on how your mpi library decides to assign threads. I
know there are some switches that you can pass to mpirun that modify this
behavior. mdrun also has the "-pin on" setting that can prevent threads
from moving around. See
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Pinning_threads_to_physical_cores

You could also try using the "-multi" and "-multidir" flags provided by
mdrun to run multiple simulations at the same time with one mdrun command.

-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group 
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
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Re: [gmx-users] DNA based protein error

[Justin Lemkul]

On 9/8/17 7:27 AM, Anjali Patel wrote:

Hello to all,

I am doing MD simulation of DNA based protein-protein complex. but getting
error is"Residue 'DT' not found in residue topology database" can anyone
help to fix this. I should change forcefield (ff)? if yes then please
suggest appropriate ff. or there is something else to change in pdb file.



What is DT and what does your force field expect it to be named? You 
should choose your force field based on which one is best suited to the 
problem at hand, not the one that happens to work the first time you get 
it to go through pdb2gmx :)


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Need help on NVT equilibration for MD simulation of Protein-RNA complex

[Justin Lemkul]

On 9/8/17 7:10 AM, Saravanan Parameswaran wrote:

​​
​Dear Simulators,,

I am new to MD simulations. I am still learning Gromacs from tutorials and
documentation.

I want to run MD simulation of protein (1700 amino acids) with ssRNA
(around 80 nucleotides) and another dsRNA/dsDNA (around 20-40 nucleotides).

I am trying to understand how protein of interest interacts with
dsDNA/dsRNA/ssDNA/ssRNA. what will be the difference in interactions when
it interacts with different dsDNA/dsRNA/ssDNA/ssRNA and mutational studies
on both protein and dsDNA/dsRNA/ssDNA/ssRNA.

And I am stuck with parameters in ‘initial phase’ NVT equilibration using
Langevin bath which I have found from literature.

I am struggling to find the exact parameters for the protein-DNA/RNA system
to run the three steps of the initial phase: (a) 10ps with increasing
temperature from 0 to 100 K keeping protein & RNA fixed, (b) 25ps with
temperature was further increased upto 200 K keeping backbone atoms of
protein & RNA fixed and (c) 25ps to reach 298 K. Then NPT equilibration for
100 ps at 298 K

After this initial phase, NPT equilibration for 40-50ns followed by
production run in microseconds.

I am not sure how to set parameters for MDP files for the three steps of
the initial phase and NPT equilibration . I have googled it for few days,
but not of much help. I end up with mdp files for free energy analysis only.


Why the NVT equilbration or initial phase is done with three steps in
Langevin bath?


There are many ways to prepare simulation systems.  Some people believe 
in slow warming of a system, others don't.



Why long runs for NPT equilibration?


You have to obtain a stable thermodynamic ensemble; I don't know why 
those authors chose such a time frame (tip: ask them, that's what 
corresponding author contact information is for) but there had to be a 
reason.



Is it really necessary to do production run in microseconds?


Depends on the questions being asked in the simulation.  You have to 
simulate on a time scale sufficient to answer whatever biological 
questions are of interest.




I request you all to provide me the ‘mdp’ files for NVT and NPT
equilibration as well as MD production to run the molecular
dynamics simulations of protein/RNA complex.


If you want to replicate exactly what the authors did, you need to apply 
what is called "simulated annealing."  It is described in the manual 
along with an example.  Custom position restraint files are generated 
with gmx genrestr.  You will need different treatment of restraints in 
each phase described above.


-Justin

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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Re: [gmx-users] Merging different topology files

[Justin Lemkul]

On 9/8/17 5:50 AM, Momin Ahmad wrote:
Thank you for your help. I already did that but i get a weird error 
that i can not solve. I attached the topology files and the error 
message. Maybe the numbering of the residues has to be changed? Thanks 
in advance.




You have lots of missing parameters, which means your force field 
doesn't know how to represent these molecules.  You are also missing 
several bonded interactions in your ammonia topology, so the simulation 
won't be stable.  As to the last fatal error, your [molecules] directive 
doesn't actually specify how many molecules you have:


[molecules]
AMMONIA
METHANE

There need to be actual numbers here.  Please go back and do some basic 
GROMACS tutorials and reading in the PDF manual (particularly Chapter 5) 
to understand topology format before trying to do something like this.  
It's very easy to make lots of mistakes, some obvious and some not.


-Justin


Cheers,

Momin


Am 07.09.2017 um 21:08 schrieb Justin Lemkul:



On 9/7/17 10:19 AM, Momin Ahmad wrote:

Hello all,

is there a simple way to merge two or more topology files into one? 
I am trying to use grompp to set up a simulation but my solvation 
contains different molecules which have different .top files. I also 
tried creating a main topology file which includes the other two 
topologies but without success. Hope anyone knows how to solve this.




The #include mechanism is the only way to do this.  If you have two 
.top (system topology) files, then:


1. Remove any #include statement for a parent force field (i.e. the 
file with [defaults] in it)

2. Remove any [system] or [molecules] directive

(you now have proper .itp format)

3. Remove any redundant #include statements (e.g. for water, ions) to 
avoid "moleculetype redefined" errors
4. Construct a new .top that #includes a parent force field, your two 
new .itp files, and has [system] and [molecules] directives.


-Justin







--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] (no subject)

[Justin Lemkul]

On 9/8/17 5:43 AM, abir paul wrote:

hi,
I am very new to gromacs. I want to see phosphorylation effect on a
protein molecule. So I have phosphorylated my protein in charmm-gui server.
when i tried to generate .gro file by using pdb2gmx command line it gives
me following error :

   Fatal error:
  Residue 1 named GLY of a molecule in the input file was mapped
  to an entry in the topology database, but the atom N used in
  an interaction of type improper in that entry is not found in
the
  input file. Perhaps your atom and/or residue naming needs to be
  fixed.

How can I fixed this error. please help me.


CHARMM-GUI will build the whole system for you, including generating the 
GROMACS topology and input files.  There's no need to run anything 
through pdb2gmx.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] DNA based protein error

[Anjali Patel]

Hello to all,

I am doing MD simulation of DNA based protein-protein complex. but getting
error is"Residue 'DT' not found in residue topology database" can anyone
help to fix this. I should change forcefield (ff)? if yes then please
suggest appropriate ff. or there is something else to change in pdb file.


With regards
Anjali Patel
Research Scholar
Department of Physics
The M S University of Baroda, Vadodara-390002
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[gmx-users] Need help on NVT equilibration for MD simulation of Protein-RNA complex

[Saravanan Parameswaran]

​​
​Dear Simulators,,

I am new to MD simulations. I am still learning Gromacs from tutorials and
documentation.

I want to run MD simulation of protein (1700 amino acids) with ssRNA
(around 80 nucleotides) and another dsRNA/dsDNA (around 20-40 nucleotides).

I am trying to understand how protein of interest interacts with
dsDNA/dsRNA/ssDNA/ssRNA. what will be the difference in interactions when
it interacts with different dsDNA/dsRNA/ssDNA/ssRNA and mutational studies
on both protein and dsDNA/dsRNA/ssDNA/ssRNA.

And I am stuck with parameters in ‘initial phase’ NVT equilibration using
Langevin bath which I have found from literature.

I am struggling to find the exact parameters for the protein-DNA/RNA system
to run the three steps of the initial phase: (a) 10ps with increasing
temperature from 0 to 100 K keeping protein & RNA fixed, (b) 25ps with
temperature was further increased upto 200 K keeping backbone atoms of
protein & RNA fixed and (c) 25ps to reach 298 K. Then NPT equilibration for
100 ps at 298 K

After this initial phase, NPT equilibration for 40-50ns followed by
production run in microseconds.

I am not sure how to set parameters for MDP files for the three steps of
the initial phase and NPT equilibration . I have googled it for few days,
but not of much help. I end up with mdp files for free energy analysis only.


Why the NVT equilbration or initial phase is done with three steps in
Langevin bath?

Why long runs for NPT equilibration?

Is it really necessary to do production run in microseconds?


I request you all to provide me the ‘mdp’ files for NVT and NPT
equilibration as well as MD production to run the molecular
dynamics simulations of protein/RNA complex.

I would be really thankful for your kind help.


With Warm Regards,

Saravanan Parameswaran

PostDoctoral Fellow

Gyeongsang National University,

South Korea
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Re: [gmx-users] Merging different topology files

[Momin Ahmad]

Thank you for your help. I already did that but i get a weird error that 
i can not solve. I attached the topology files and the error message. 
Maybe the numbering of the residues has to be changed? Thanks in advance.


Cheers,

Momin


Am 07.09.2017 um 21:08 schrieb Justin Lemkul:



On 9/7/17 10:19 AM, Momin Ahmad wrote:

Hello all,

is there a simple way to merge two or more topology files into one? I 
am trying to use grompp to set up a simulation but my solvation 
contains different molecules which have different .top files. I also 
tried creating a main topology file which includes the other two 
topologies but without success. Hope anyone knows how to solve this.




The #include mechanism is the only way to do this.  If you have two 
.top (system topology) files, then:


1. Remove any #include statement for a parent force field (i.e. the 
file with [defaults] in it)

2. Remove any [system] or [molecules] directive

(you now have proper .itp format)

3. Remove any redundant #include statements (e.g. for water, ions) to 
avoid "moleculetype redefined" errors
4. Construct a new .top that #includes a parent force field, your two 
new .itp files, and has [system] and [molecules] directives.


-Justin



:-) GROMACS - gmx grompp, 2016.3 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar Bjelkmar   
 Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit Groenhof  
 Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios Karkoulis
Peter KassonJiri Kraus  Carsten Kutzner  Per Larsson
  Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik Marklund   
   Teemu Murtola   Szilard Pall   Sander Pronk  Roland Schulz   
  Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman  
  Teemu Virolainen  Christian WennbergMaarten Wolf   
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2017, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx grompp, version 2016.3
Executable:   /usr/local/bin/gmx
Data prefix:  /usr/local
Working dir:  /home/momin/work/click-chemistry/simulation
Command line:
  gmx grompp -f minim.mdp -c system_solv.gro -p topol.top -o system.tpr


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14#

NOTE 1 [file minim.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 61641030
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations

ERROR 1 [file methane_custom.itp, line 16]:
  No default Bond types


ERROR 2 [file methane_custom.itp, line 17]:
  No default Bond types


ERROR 3 [file methane_custom.itp, line 18]:
  No default Bond types


ERROR 4 [file methane_custom.itp, line 19]:
  No default Bond types


ERROR 5 [file methane_custom.itp, line 23]:
  No default Angle types


ERROR 6 [file methane_custom.itp, line 24]:
  No default Angle types


ERROR 7 [file methane_custom.itp, line 25]:
  No default Angle types


ERROR 8 [file methane_custom.itp, line 26]:
  No default Angle types


ERROR 9 [file methane_custom.itp, line 27]:
  No default Angle types


ERROR 10 [file methane_custom.itp, line 28]:
  No default Angle types


WARNING 1 [file topol.top, line 18]:
  Too few parameters on line (source file
  /home/momin/gromacs-2016.3/src/gromacs/gmxpreprocess/toppush.cpp, line
  2377)

Excluding 3 bonded neighbours molecule type 'METHANE'

WARNING 2 [file topol.top, line 19]:
  Too few parameters on line (source file
  /home/momin/gromacs-2016.3/src/gromacs/gmxpreprocess/toppush.cpp, line
  2377)

Excluding 3 bonded neighbours molecule type 'METHANE'

---
Program: gmx grompp, version 2016.3
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 612)

Fatal error:
number of coordinates in coordinate file (system_solv.gro, 113)
 does not match topology (topol.top, 10)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

; main topology file
;
; Include force-field
#include "amber99sb-ildn.ff/forcefield.itp"

;Include topologies
#includ

[gmx-users] (no subject)

[abir paul]

hi,
   I am very new to gromacs. I want to see phosphorylation effect on a
protein molecule. So I have phosphorylated my protein in charmm-gui server.
when i tried to generate .gro file by using pdb2gmx command line it gives
me following error :

  Fatal error:
 Residue 1 named GLY of a molecule in the input file was mapped
 to an entry in the topology database, but the atom N used in
 an interaction of type improper in that entry is not found in
the
 input file. Perhaps your atom and/or residue naming needs to be
 fixed.

How can I fixed this error. please help me.
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[gmx-users] On the setting tau_t for SD integrator for membrane protein simulation

[Own 12121325]

Dear Gromacs users!

I would like to use Langevin's thermostat in my simulation of the membrane
protein. I am interesting what values of tau_t will be appropriate for such
simulation, assuming that I would like to create a "soft" equilibration
conditions with slower relaxation times via coupling of the system to the
medium with higher viscosity.

Thanks!

Micky
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Re: [gmx-users] purpose of step pdb files during MD

[Vedat Durmaz]

Am 07.09.2017 um 21:10 schrieb Justin Lemkul:
>
> On 9/7/17 10:29 AM, Vedat Durmaz wrote:
>> i really appreciate this pretty informative answer. and do you also know, 
>> what the infix "n254" or "n2" stands for?
> Node ID.
>
>> what i found strange is that the error occurs after nearly 10M MD steps. in 
>> other copies of the same system, the error doesn't occur at all even after 
>> the entire predefines time span (40ns).
>>
>> it's a long fibril chain (>200 repeating units) of a 7mer polypeptide. the 
>> walls of the triclinic simulation box of size 10x8x70 nm have an initial 
>> distance of 1.5 nm to the fibril and i have chosen "comm-mode  = linear" in 
>> order to keep the system centered. i'm actually wondering, whether that 
>> might have caused the error or whether the system will for sure crash if the 
>> long chain changes its shape to some spheric one that doesn't fit the slim 
>> box anymore.
>>
>> do you have any experience with that?
> Nope, sorry.  A crash after a long simulation time is very unusual and 
> hard to diagnose.  Normally things fail rather quickly.  Does your 
> GROMACS installation pass all regression tests?
>
> -Justin
>

ok. since i haven't compiled this gromacs installation i haven't seen any 
results of its test runs. anyway, i carried out the simulations again and this 
time no error occurred.

thanks again for your help!

vedat


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