Re: [gmx-users] Ligand interaction

[rama david]

Dear md kashif,
 my protein energy is
-1.5e+06 and now after docking with ligand it becomes -1.05e+06.
what does it mean?

is it is the energy of ligand_protein complex or simply the protein???

In docking  generally the receptor is rigid, then why the receptor will
change its energy ?? the energy of receptor,free  drug  and receptor-drug
complex
will different.


With best regards


On Wed, Nov 12, 2014 at 9:57 AM, md kashif 
wrote:

> Hello everyone
> please suggest me that is there any change in protein energy after docking
> the ligand to my energy minimized protein? my protein energy is
> -1.5e+06 and now after docking with ligand it becomes -1.05e+06.
> what does it mean?
>
>
> Thanks
> --
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[gmx-users] Ligand interaction

[md kashif]

Hello everyone
please suggest me that is there any change in protein energy after docking
the ligand to my energy minimized protein? my protein energy is
-1.5e+06 and now after docking with ligand it becomes -1.05e+06.
what does it mean?


Thanks
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Re: [gmx-users] lipid molecules are overlapping with proteinmolecule

[Padmani Sandhu]

hello justin,

Energy minimization is not converging to Fmax in 2 steps in between
shrinking steps. I tried it for 5 steps also, What can I do to resolve
it..???



Regards,

Padmani

On Tue, Nov 11, 2014 at 6:08 PM, Justin Lemkul  wrote:

>  [image: Boxbe]  This message is eligible
> for Automatic Cleanup! (jalem...@vt.edu) Add cleanup rule
> 
> | More info
> 
>
>
>
> On 11/11/14 6:45 AM, Padmani Sandhu wrote:
>
>> Hello all,
>>
>>
>> I am trying to energy minimize a trimeric protein in DPPC bilayer but
>> facing problem in reaching desired lipid per area using "inflategro.pl".
>> After 5 or 6 steps of shrinking and energy minimization lipids molecules
>> start interfering with protein. I tried to increase cutt-off, but that is
>> also giving error during grompp.
>>
>>
> Proper energy minimization between shrinking steps should eliminate this.
>
> -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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-- 
*Padmani sandhu*
*Research Scholar,*
*Center for Computational Biology and Bioinformatics,*
*Central University of Himachal Pradesh,*
*Temporary Academic Block, Shahpur *
*Pin 176206, District Kangra,*
*Himachal Pradesh, India*
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Re: [gmx-users] New problem GROMACS 4.6.7 in Intel Cluster

[Justin Lemkul]

On 11/11/14 8:59 PM, Agnivo Gosai wrote:

Dear Users

I thought that using MPI OFF commands in cmake will solve my problem. So I
used the following command :

-bash-4.1$ /work/gb_lab/agosai/GROMACS/cmake-2.8.11/bin/cmake ..
-DGMX_BUILD_OWN_FFTW=ON
-DCMAKE_INSTALL_PREFIX=/work/gb_lab/agosai/gmx465serial
-DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_THREAD_MPI=off
-DGMX_MPI=off

However "genbox" is still failing with the same error i.e.
OMP: Error #178: Function pthread_getattr_np failed:
OMP: System error #12: Cannot allocate memory
Aborted

I read Dr. Mark 's comments and Dr Justin's comments in the trailing mail.
But I am not sure what is to be done. Can anyone lay down a procedure for
fixing this. I am sorry if I am asking too much but it will be of great
help.



This is probably a question best asked of your sysadmin, who should know how to 
execute jobs on your cluster (so please ask your sysadmin).  But if you want any 
advice from this community, you'll need to provide the exact command you're 
trying to issue, and the full job script if it's being submitted to a queuing 
system.  Something is wrong with the environment or the invocation of the 
command.  Serial commands like preprocessing and analysis tools should be 
totally independent of any type of configured parallelization.


-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] New problem GROMACS 4.6.7 in Intel Cluster

[Agnivo Gosai]

Dear Users

I thought that using MPI OFF commands in cmake will solve my problem. So I
used the following command :

-bash-4.1$ /work/gb_lab/agosai/GROMACS/cmake-2.8.11/bin/cmake ..
-DGMX_BUILD_OWN_FFTW=ON
-DCMAKE_INSTALL_PREFIX=/work/gb_lab/agosai/gmx465serial
-DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_THREAD_MPI=off
-DGMX_MPI=off

However "genbox" is still failing with the same error i.e.
OMP: Error #178: Function pthread_getattr_np failed:
OMP: System error #12: Cannot allocate memory
Aborted

I read Dr. Mark 's comments and Dr Justin's comments in the trailing mail.
But I am not sure what is to be done. Can anyone lay down a procedure for
fixing this. I am sorry if I am asking too much but it will be of great
help.


-- Forwarded message --
From: Mark Abraham 
To: Discussion list for GROMACS users 
Cc:
Date: Mon, 10 Nov 2014 02:26:09 +0100
Subject: Re: [gmx-users] New problem GROMACS 4.6.7 in Intel Cluster
On Mon, Nov 10, 2014 at 2:17 AM, Justin Lemkul  wrote:

>
>
> On 11/9/14 8:15 PM, Agnivo Gosai wrote:
>
>> Dear Users
>>
>> Firstly thanks (specially Drs. Szilard and Mark ) for helping me out with
>> the installation of GROMACS 4.6.7 on my university Intel cluster. However
>> I
>> ran into a new problem while using it.
>>
>> 1. Firstly I used pdb2gmx to process a pdb file.
>> 2. Then I used editconf.
>> 3. Then I used genbox.
>>
>> But I encountered with the following error.
>>
>> Initialising van der waals distances...
>> Will generate new solvent configuration of 5x5x9 boxes
>> Generating configuration
>> Sorting configuration
>> Found 1 molecule type:
>>  SOL (   3 atoms): 48600 residues
>> Calculating Overlap...
>> box_margin = 0.315
>> Removed 53454 atoms that were outside the box
>> OMP: Error #178: Function pthread_getattr_np failed:
>> OMP: System error #12: Cannot allocate memory
>> Aborted
>>
>> Now upon searching on the web it seems to be an OpenMP error. Again I am
>> in
>> a fix which I have little or no idea about.
>>
>>
> Preprocessing tools (and most analysis tools) are not parallelized in any
> way. They run on one core only.  Generally you do not carry out these
sorts
> of operations on a cluster, as there is no benefit to doing so.
>

True, and the particular problem is likely that Agnivo has not prepared the
environment correctly, e.g. by sourcing Intel's compilervars.sh script,
and/or following the cluster's usage guide for loading its Intel module.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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Re: [gmx-users] restarting of shifted potential, 4.6.7 bug?

[Johnny Lu]

Going from non-shift to shifted potential changes the energy. So I was not
surprised by the sudden jump of energy between step 0 and step 10 for the
previous simulation (npt14).

But the jump near step 0 for the current simulation (npt15) is not right.

This is an equilibration run.

I have just uploaded the files at http://redmine.gromacs.org/issues/1640


On Tue, Nov 11, 2014 at 10:54 AM, Mark Abraham 
wrote:

> On Tue, Nov 11, 2014 at 3:38 PM, Johnny Lu  wrote:
>
> > Hi.
> >
> > I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing
> > from a NPT without Potential-shift-Verlet. The energy dropped from -3e5
> to
> > -4e5, which is fine.
> >
> > After that, I continue the 30ns NPT with the same mdp file, except with a
> > longer run time (300ns).
> >
> > The total energy was -4e5 at step 0, and then -3e5 at step 5000, and now
> at
> > about 25 ns, it goes back to -3.5e5. Why the energy suddenly changed
> after
> > step 0?
> >
>
> IIRC, the restart ought to compute the same energy on the initial
> coordinates as it did at the end of the previous run, and even if there's
> no re-computation on the same coordinates, obviously it should not  jump by
> 1e5 in a few steps (or one? can't tell from the resolution). I would think
> that might be a bug in filling a data structure for the output, but
> probably not one in the simulation itself. Please file an issue at
> http://redmine.gromacs.org, tarballing all the relevant files, and I'll
> try
> to look at it.
>
> The long-time behaviour of both simulations is pretty suspect though. Since
> you're prepared to be ultra-conservative with your non-bonded and SETTLE
> settings, I would explore using a 0.5fs time step (in normal and
> ultra-conservative mode). Berendsen is not a good barostat algorithm for
> production work, too... but I would not expect such a problem from its use.
> Perhaps more importantly, why are you turning off the long-range dispersion
> correction?
>
> Mark
>
> I used the same machine and same mixed precision gromacs 4.6.7 mdrun and
> > grompp for both simulations.
> >
> > The plot of total energies for the two simulations:
> > http://oi60.tinypic.com/ddmejd.jpg
> > The two mdp files: http://oi58.tinypic.com/11980si.jpg
> >
> > The commands that I used for continuing the simulations:
> >
> > The previous simulation (npt14): ../../sofware/gromacs-4.6.7/bin/grompp
> -f
> > npt14.mdp -c npt13.tpr -t npt13_step22620750.cpt -o npt14.tpr
> >
> > The current simulation (npt15): ../../sofware/gromacs-4.6.7/bin/grompp -f
> > npt15.mdp -c npt14.tpr -t npt14_step3000.cpt -o npt15.tpr
> >
> > Thanks.
> > --
> > Gromacs Users mailing list
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Re: [gmx-users] restarting of shifted potential, 4.6.7 bug?

[Mark Abraham]

On Tue, Nov 11, 2014 at 3:38 PM, Johnny Lu  wrote:

> Hi.
>
> I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing
> from a NPT without Potential-shift-Verlet. The energy dropped from -3e5 to
> -4e5, which is fine.
>
> After that, I continue the 30ns NPT with the same mdp file, except with a
> longer run time (300ns).
>
> The total energy was -4e5 at step 0, and then -3e5 at step 5000, and now at
> about 25 ns, it goes back to -3.5e5. Why the energy suddenly changed after
> step 0?
>

IIRC, the restart ought to compute the same energy on the initial
coordinates as it did at the end of the previous run, and even if there's
no re-computation on the same coordinates, obviously it should not  jump by
1e5 in a few steps (or one? can't tell from the resolution). I would think
that might be a bug in filling a data structure for the output, but
probably not one in the simulation itself. Please file an issue at
http://redmine.gromacs.org, tarballing all the relevant files, and I'll try
to look at it.

The long-time behaviour of both simulations is pretty suspect though. Since
you're prepared to be ultra-conservative with your non-bonded and SETTLE
settings, I would explore using a 0.5fs time step (in normal and
ultra-conservative mode). Berendsen is not a good barostat algorithm for
production work, too... but I would not expect such a problem from its use.
Perhaps more importantly, why are you turning off the long-range dispersion
correction?

Mark

I used the same machine and same mixed precision gromacs 4.6.7 mdrun and
> grompp for both simulations.
>
> The plot of total energies for the two simulations:
> http://oi60.tinypic.com/ddmejd.jpg
> The two mdp files: http://oi58.tinypic.com/11980si.jpg
>
> The commands that I used for continuing the simulations:
>
> The previous simulation (npt14): ../../sofware/gromacs-4.6.7/bin/grompp -f
> npt14.mdp -c npt13.tpr -t npt13_step22620750.cpt -o npt14.tpr
>
> The current simulation (npt15): ../../sofware/gromacs-4.6.7/bin/grompp -f
> npt15.mdp -c npt14.tpr -t npt14_step3000.cpt -o npt15.tpr
>
> Thanks.
> --
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Re: [gmx-users] Fwd: Re: Frequency dependent dielectric constant

[Bharat Sharma]

Hello,
I have managed to get dielectric constant. But it gives for very high
frequency range. I am interested in low frequency range (typically less
than 1000 GHz). How do I control range of frequency while calling
g_dielectric function?

Thank you.

Bharat

On Thu, Nov 6, 2014 at 4:44 PM, David van der Spoel 
wrote:

> On 2014-11-06 22:28, David van der Spoel wrote:
>
>>
>>
>>
>>  Original Message 
>> Subject: Re: [gmx-users] Frequency dependent dielectric constant
>> Date: Thu, 6 Nov 2014 16:23:34 -0500
>> From: Bharat Sharma 
>> To: sp...@xray.bmc.uu.se
>>
>>
>>
>> Hello Professor David,
>> Sorry for sending you a private email.
>> Thank you for your reply on forum. Is it possible to use external dipole
>> moment file which has" t Mx My Mz " data to calculate autocorrelation
>> function which is defined as phi (t) =  / ^2.
>> Autocorrelation file is necessary to use g_dielectric function.
>>
>>  Looks like you have not run
> gmx dielectric -h
> You need the acf which you can produce using gmx dipoles
>
>
>  Thank you.
>>
>> Sincerely,
>> Bharat Sharma
>>
>> I have a file like this.
>>
>> 1  -18.4054002593869  -8.63550624406573  13.1822307410726
>> 2  -16.3448281386543  -9.26825538523777  12.6970594193942
>> 3  -16.2122319636283  -9.584079278168  10.1880749346946
>> 4  -16.8000261232119  -9.3544161158981  9.292811661397
>> 5  -16.9675609841484  -8.06386828149236  9.04336117783739
>> 6  -16.705420659386  -8.15253302392368  6.35375835558321
>> 7  -16.3482274903309  -7.42833201686778  2.40403368273462
>> 8  -17.6089611732605  -6.5810524629  1.0191769956
>> 9  -19.1340573022822  -7.31608247201016  1.0593505375146
>> 10  -18.8898972984193  -8.50162965184524  -0.390241915321422
>> 11  -17.3201971209895  -8.88827721892198  -2.91666461388975
>> 12  -17.9697387584415  -10.3820791259894  -3.09327709524195
>> 13  -19.4150366450719  -12.5922697307389  -1.76640044899152
>> 14  -17.2192770802751  -12.719093017379  -1.76633521518987
>> 15  -13.9887596873511  -11.6333686786579  -2.53760673124873
>> 16  -15.631174760539  -11.8671822022606  -1.04251159658716
>> 17  -19.7752453695527  -13.1793702340658  0.669842005269544
>> 18  -20.5031312769212  -12.8221354246758  1.7010916111
>> 19  -20.1714747689171  -11.5235359847683  3.12874014505405
>> 20  -23.4993319248317  -11.1069526872016  5.40262656219366
>> 21  -26.9810468267155  -10.3960073112131  6.66596873251908
>> 22  -25.2970021256126  -8.26285916407095  6.85639239972755
>> 23  -22.3727114023644  -7.29618209094124  7.96149529066325
>> 24  -22.8378886264605  -7.94207228198017  9.4631219697683
>> 25  -23.9479347882939  -8.18332794071831  8.90226933404197
>> 26  -23.4431023794441  -8.57868882479158  7.48452761101869
>> 27  -23.8923601075312  -9.80575680710948  7.74832733959732
>> 28  -26.2650526524463  -11.6213772988559  7.80737869303804
>> 29  -28.726262739164  -11.5765264683748  3.98968339600384
>> 30  -28.8118374367959  -10.5568670286443  1.98998557532743
>>
>>
>>
>> On Thu, Nov 6, 2014 at 2:08 PM, David van der Spoel
>> mailto:sp...@xray.bmc.uu.se>> wrote:
>>
>>  On 2014-11-06 19:33, Bharat Sharma wrote:
>>
>>  Hello,
>>
>>  It's a friendly reminder if someone knows how to calculate.
>>  Please let me
>>  know.
>>
>>  g_dielectric.
>>
>>
>>  Thank you.
>>
>>  Bharat
>>
>>
>>
>>  --
>>  David van der Spoel, Ph.D., Professor of Biology
>>  Dept. of Cell & Molec. Biol., Uppsala University.
>>  Box 596, 75124 Uppsala, Sweden. Phone: +46184714205
>>  .
>>  sp...@xray.bmc.uu.se 
>>  http://folding.bmc.uu.se
>>  --
>>  Gromacs Users mailing list
>>
>>  * Please search the archive at
>>  http://www.gromacs.org/__Support/Mailing_Lists/GMX-__Users_List
>>   before
>>  posting!
>>
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>>  
>>
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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
>>  .
>>
>>
>>
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
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* Please 

Re: [gmx-users] restarting of shifted potential, 4.6.7 bug?

[Johnny Lu]

The system has 30k water and a protein with ~170 amino acid.
Here are the PME tuning:

npt14:
DD  step 4 load imb.: force 58.1%

step   10: timed with pme grid 80 80 80, coulomb cutoff 1.000: 37.1 M-cycles
step   20: timed with pme grid 64 64 64, coulomb cutoff 1.173: 32.6 M-cycles
step   30: timed with pme grid 56 56 56, coulomb cutoff 1.341: 34.5 M-cycles
step   40: timed with pme grid 48 48 48, coulomb cutoff 1.564: 40.7 M-cycles
step   50: timed with pme grid 72 72 72, coulomb cutoff 1.043: 33.9 M-cycles
step   60: timed with pme grid 64 64 64, coulomb cutoff 1.173: 32.2 M-cycles
step   70: timed with pme grid 60 60 60, coulomb cutoff 1.251: 32.8 M-cycles
step   80: timed with pme grid 56 56 56, coulomb cutoff 1.341: 32.2 M-cycles
step   90: timed with pme grid 52 52 52, coulomb cutoff 1.444: 32.2 M-cycles
step  100: timed with pme grid 72 72 72, coulomb cutoff 1.043: 33.8 M-cycles
step  110: timed with pme grid 64 64 64, coulomb cutoff 1.173: 40.3 M-cycles
step  120: timed with pme grid 60 60 60, coulomb cutoff 1.251: 32.4 M-cycles
step  130: timed with pme grid 56 56 56, coulomb cutoff 1.341: 33.0 M-cycles
step  140: timed with pme grid 52 52 52, coulomb cutoff 1.444: 32.1 M-cycles
  optimal pme grid 52 52 52, coulomb cutoff 1.444
DD  step 4999 load imb.: force 55.3%

npt15:

DD  step 4 load imb.: force 41.2%

step   10: timed with pme grid 80 80 80, coulomb cutoff 1.000: 36.6 M-cycles
step   20: timed with pme grid 64 64 64, coulomb cutoff 1.181: 32.9 M-cycles
step   30: timed with pme grid 56 56 56, coulomb cutoff 1.350: 33.6 M-cycles
step   40: timed with pme grid 48 48 48, coulomb cutoff 1.575: 33.2 M-cycles
step   50: timed with pme grid 44 44 44, coulomb cutoff 1.718: 35.8 M-cycles
step   60: timed with pme grid 40 40 40, coulomb cutoff 1.890: 40.8 M-cycles
step   70: timed with pme grid 80 80 80, coulomb cutoff 1.000: 36.5 M-cycles
step   80: timed with pme grid 72 72 72, coulomb cutoff 1.050: 33.8 M-cycles
step   90: timed with pme grid 64 64 64, coulomb cutoff 1.181: 32.0 M-cycles
step  100: timed with pme grid 60 60 60, coulomb cutoff 1.260: 32.3 M-cycles
step  110: timed with pme grid 56 56 56, coulomb cutoff 1.350: 31.6 M-cycles
step  120: timed with pme grid 52 52 52, coulomb cutoff 1.454: 32.1 M-cycles
step  130: timed with pme grid 48 48 48, coulomb cutoff 1.575: 32.3 M-cycles
step  140: timed with pme grid 44 44 44, coulomb cutoff 1.718: 35.3 M-cycles
step  150: timed with pme grid 42 42 42, coulomb cutoff 1.800: 37.7 M-cycles
step  160: timed with pme grid 72 72 72, coulomb cutoff 1.050: 33.5 M-cycles
step  170: timed with pme grid 64 64 64, coulomb cutoff 1.181: 32.0 M-cycles
step  180: timed with pme grid 60 60 60, coulomb cutoff 1.260: 31.9 M-cycles
step  190: timed with pme grid 56 56 56, coulomb cutoff 1.350: 31.4 M-cycles
step  200: timed with pme grid 52 52 52, coulomb cutoff 1.454: 31.6 M-cycles
step  210: timed with pme grid 48 48 48, coulomb cutoff 1.575: 32.0 M-cycles
  optimal pme grid 56 56 56, coulomb cutoff 1.350
DD  step 4999 load imb.: force 41.0%





On Tue, Nov 11, 2014 at 9:44 AM, Johnny Lu  wrote:

> by the way, the machine has 4 Tesla K40m gpu, 32 xeon cpu with avx, and i
> ran: nohup ../../mdrun -deffnm npt15 -cpt 1 -cpnum &
>
> On Tue, Nov 11, 2014 at 9:38 AM, Johnny Lu  wrote:
>
>> Hi.
>>
>> I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing
>> from a NPT without Potential-shift-Verlet. The energy dropped from -3e5 to
>> -4e5, which is fine.
>>
>> After that, I continue the 30ns NPT with the same mdp file, except with a
>> longer run time (300ns).
>>
>> The total energy was -4e5 at step 0, and then -3e5 at step 5000, and now
>> at about 25 ns, it goes back to -3.5e5. Why the energy suddenly changed
>> after step 0?
>>
>> I used the same machine and same mixed precision gromacs 4.6.7 mdrun and
>> grompp for both simulations.
>>
>> The plot of total energies for the two simulations:
>> http://oi60.tinypic.com/ddmejd.jpg
>> The two mdp files: http://oi58.tinypic.com/11980si.jpg
>>
>> The commands that I used for continuing the simulations:
>>
>> The previous simulation (npt14): ../../sofware/gromacs-4.6.7/bin/grompp
>> -f npt14.mdp -c npt13.tpr -t npt13_step22620750.cpt -o npt14.tpr
>>
>> The current simulation (npt15): ../../sofware/gromacs-4.6.7/bin/grompp -f
>> npt15.mdp -c npt14.tpr -t npt14_step3000.cpt -o npt15.tpr
>>
>> Thanks.
>>
>>
>
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Re: [gmx-users] restarting of shifted potential, 4.6.7 bug?

[Johnny Lu]

by the way, the machine has 4 Tesla K40m gpu, 32 xeon cpu with avx, and i
ran: nohup ../../mdrun -deffnm npt15 -cpt 1 -cpnum &

On Tue, Nov 11, 2014 at 9:38 AM, Johnny Lu  wrote:

> Hi.
>
> I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing
> from a NPT without Potential-shift-Verlet. The energy dropped from -3e5 to
> -4e5, which is fine.
>
> After that, I continue the 30ns NPT with the same mdp file, except with a
> longer run time (300ns).
>
> The total energy was -4e5 at step 0, and then -3e5 at step 5000, and now
> at about 25 ns, it goes back to -3.5e5. Why the energy suddenly changed
> after step 0?
>
> I used the same machine and same mixed precision gromacs 4.6.7 mdrun and
> grompp for both simulations.
>
> The plot of total energies for the two simulations:
> http://oi60.tinypic.com/ddmejd.jpg
> The two mdp files: http://oi58.tinypic.com/11980si.jpg
>
> The commands that I used for continuing the simulations:
>
> The previous simulation (npt14): ../../sofware/gromacs-4.6.7/bin/grompp -f
> npt14.mdp -c npt13.tpr -t npt13_step22620750.cpt -o npt14.tpr
>
> The current simulation (npt15): ../../sofware/gromacs-4.6.7/bin/grompp -f
> npt15.mdp -c npt14.tpr -t npt14_step3000.cpt -o npt15.tpr
>
> Thanks.
>
>
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[gmx-users] restarting of shifted potential, 4.6.7 bug?

[Johnny Lu]

Hi.

I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing
from a NPT without Potential-shift-Verlet. The energy dropped from -3e5 to
-4e5, which is fine.

After that, I continue the 30ns NPT with the same mdp file, except with a
longer run time (300ns).

The total energy was -4e5 at step 0, and then -3e5 at step 5000, and now at
about 25 ns, it goes back to -3.5e5. Why the energy suddenly changed after
step 0?

I used the same machine and same mixed precision gromacs 4.6.7 mdrun and
grompp for both simulations.

The plot of total energies for the two simulations:
http://oi60.tinypic.com/ddmejd.jpg
The two mdp files: http://oi58.tinypic.com/11980si.jpg

The commands that I used for continuing the simulations:

The previous simulation (npt14): ../../sofware/gromacs-4.6.7/bin/grompp -f
npt14.mdp -c npt13.tpr -t npt13_step22620750.cpt -o npt14.tpr

The current simulation (npt15): ../../sofware/gromacs-4.6.7/bin/grompp -f
npt15.mdp -c npt14.tpr -t npt14_step3000.cpt -o npt15.tpr

Thanks.
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Re: [gmx-users] GROMACS 5 - problem with LINCS with freeze groups

[Tomek Wlodarski]

Hi Mark,

Thank you for replay.
I just checked this in Gromacs-4.6.7 and like you predicted I got same
LINCS warning.
I will fill bug report.
Best,

tomek

On Tue, Nov 11, 2014 at 1:41 PM, Mark Abraham 
wrote:

> Hi,
>
> You are using settings that trigger the group-scheme twin-range code.
> There's been a code bug there for a very long time, which we fixed after
> 4.6.5 (see http://redmine.gromacs.org/issues/1400. "Normal" usage such as
> in your .mdp file also tended to be broken when simulating water, which
> masked the code bug; your 4.6.5 run may look smooth, but probably the
> thermostat is hiding the systematic problem of nstlist*dt being too large
> to properly model water libration, and the symptoms of the virial problem
> we fixed are lost in the noise.
>
> If you can try 4.6.7, I expect that you will observe the same problems you
> see in 5.0.x. That will help us know what to consider fixing. We certainly
> didn't test the freeze-group functionality, so we could well have
> introduced a new problem, such as adding force components that were already
> zeroed for freezing. If I'm right about 4.6.7 also being broken, please
> file an issue at http://redmine.gromacs.org with a tarball of your grompp
> input files.
>
> Mark
>
> On Tue, Nov 11, 2014 at 2:05 PM, Tomek Wlodarski <
> tomek.wlodar...@gmail.com>
> wrote:
>
> > Hi,
> >
> > I experience some strange behaviour and I wonder if this is a bug or I am
> > doing something wrong.
> > I am running test simulation to check freeze groups in new gromacs.
> > And I am getting LINCS Warnings for atoms which should be frozen...:
> >
> > Step 0, time 0 (ps)  LINCS WARNING
> > relative constraint deviation after LINCS:
> > rms nan, max inf (between atoms 30 and 31)
> > bonds that rotated more than 30 degrees:
> >  atom 1 atom 2  angle  previous, current, constraint length
> >  32 33   90.80.1010  23.4699  0.1010
> >  32 34   90.30.1010  71.2488  0.1010
> > [...]
> >
> > my mdp file:
> >
> > ; RUN CONTROL PARAMETERS
> > integrator   = md
> > dt   = 0.002   ; 2 femtosecond time step for
> > integration
> > nsteps   = 50  ; 1ns
> >
> > ; OUTPUT CONTROL OPTIONS
> > nstxout  = 5000; save coordinates every 2 ps
> > nstvout  = 5000; save velocities every 2 ps
> > nstenergy = 5000; save energies every 2 ps
> > nstlog   = 5000; update log file every 2 ps
> > energygrps   = Protein Non-Protein
> > nstxtcout= 5000
> > xtc-grps = non-Water
> >
> > ; NEIGHBORSEARCHING PARAMETERS
> > nstlist  = 5
> > ns-type  = Grid
> > cutoff-scheme= group
> > pbc  = xyz
> > rlist= 0.9
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > coulombtype  = pme
> > rcoulomb = 0.9
> > fourierspacing   = 0.12
> > ewald_rtol = 1e-5
> > fourier_nx   = 0
> > fourier_ny   = 0
> > fourier_nz   = 0
> > optimize_fft = yes
> > vdw-type = Cut-off
> > rvdw = 1.2
> > energygrp_table =
> >
> > ; Temperature coupling
> > Tcoupl   = V-rescale
> > tc-grps  = ProteinNon-Protein
> > tau_t= 0.10.1
> > ref_t= 300300
> >
> > ; Freeze atoms
> > freezegrps   = Protein
> > freezedim= Y Y Y
> > energygrp-excl   = Protein Protein
> >
> > ; Pressure coupling
> > pcoupl   = no
> >
> > ;Velocity generation
> > gen_vel  = no
> > gen_temp = 300
> > gen_seed = -1
> >
> > ;Constrain all bonds
> > constraints = all-bonds
> > constraint-algorithm = Lincs
> > lincs_iter  = 2 ; accuracy of LINCS
> > lincs_order  = 6; also related to accuracy
> >
> > Exactly the same system with the same mdp file I am running in Gromacs
> > 4.6.5 and everything runs smoothly.
> > Any suggestions?
> > Thanks a lot!
> > Best
> >
> > tomek
> > --
> > 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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* Pleas

Re: [gmx-users] GROMACS 5 - problem with LINCS with freeze groups

[Mark Abraham]

Hi,

You are using settings that trigger the group-scheme twin-range code.
There's been a code bug there for a very long time, which we fixed after
4.6.5 (see http://redmine.gromacs.org/issues/1400. "Normal" usage such as
in your .mdp file also tended to be broken when simulating water, which
masked the code bug; your 4.6.5 run may look smooth, but probably the
thermostat is hiding the systematic problem of nstlist*dt being too large
to properly model water libration, and the symptoms of the virial problem
we fixed are lost in the noise.

If you can try 4.6.7, I expect that you will observe the same problems you
see in 5.0.x. That will help us know what to consider fixing. We certainly
didn't test the freeze-group functionality, so we could well have
introduced a new problem, such as adding force components that were already
zeroed for freezing. If I'm right about 4.6.7 also being broken, please
file an issue at http://redmine.gromacs.org with a tarball of your grompp
input files.

Mark

On Tue, Nov 11, 2014 at 2:05 PM, Tomek Wlodarski 
wrote:

> Hi,
>
> I experience some strange behaviour and I wonder if this is a bug or I am
> doing something wrong.
> I am running test simulation to check freeze groups in new gromacs.
> And I am getting LINCS Warnings for atoms which should be frozen...:
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms nan, max inf (between atoms 30 and 31)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>  32 33   90.80.1010  23.4699  0.1010
>  32 34   90.30.1010  71.2488  0.1010
> [...]
>
> my mdp file:
>
> ; RUN CONTROL PARAMETERS
> integrator   = md
> dt   = 0.002   ; 2 femtosecond time step for
> integration
> nsteps   = 50  ; 1ns
>
> ; OUTPUT CONTROL OPTIONS
> nstxout  = 5000; save coordinates every 2 ps
> nstvout  = 5000; save velocities every 2 ps
> nstenergy = 5000; save energies every 2 ps
> nstlog   = 5000; update log file every 2 ps
> energygrps   = Protein Non-Protein
> nstxtcout= 5000
> xtc-grps = non-Water
>
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist  = 5
> ns-type  = Grid
> cutoff-scheme= group
> pbc  = xyz
> rlist= 0.9
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype  = pme
> rcoulomb = 0.9
> fourierspacing   = 0.12
> ewald_rtol = 1e-5
> fourier_nx   = 0
> fourier_ny   = 0
> fourier_nz   = 0
> optimize_fft = yes
> vdw-type = Cut-off
> rvdw = 1.2
> energygrp_table =
>
> ; Temperature coupling
> Tcoupl   = V-rescale
> tc-grps  = ProteinNon-Protein
> tau_t= 0.10.1
> ref_t= 300300
>
> ; Freeze atoms
> freezegrps   = Protein
> freezedim= Y Y Y
> energygrp-excl   = Protein Protein
>
> ; Pressure coupling
> pcoupl   = no
>
> ;Velocity generation
> gen_vel  = no
> gen_temp = 300
> gen_seed = -1
>
> ;Constrain all bonds
> constraints = all-bonds
> constraint-algorithm = Lincs
> lincs_iter  = 2 ; accuracy of LINCS
> lincs_order  = 6; also related to accuracy
>
> Exactly the same system with the same mdp file I am running in Gromacs
> 4.6.5 and everything runs smoothly.
> Any suggestions?
> Thanks a lot!
> Best
>
> tomek
> --
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> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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Re: [gmx-users] Question about "Lysozyme in Water" tutorial by Dr. Lemkul

[Smith, Micholas D.]

Two things to check: First try converting your trajectory to a pdb using 
trjconv instead of avogadro, as you can taken into account the perodic 
boundries. Second, ions can behave "oddly" in simulations due to 
hydration-effects; however, having them all cluster in a location is typically 
bad, as such  it is a good idea to check that the force-field and water model 
you are using are compatible with the concentration of ions you are using 
(typically you don't want to go above 0.5M if you can help it), a quick search 
in the literature should pull up some papers on this (I seem to have misplaced 
my copies at the moment).

===
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 Nima Soltani 

Sent: Monday, November 10, 2014 7:33 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Question about "Lysozyme in Water" tutorial by Dr. Lemkul

Hi everyone
I am following excellent Gromacs tutorial that is provided by Dr. Justin
Lemkul, First of all i want to thank him for taking time to provide such an
excellent tutorial.
My Question is about final structure of protein and ions after runing final
Molecular Dynamic simulation of the last step
Here is link of my final structure that i get after simulation -after
converting it from .gro file to .pdb file (by Avogadro program):
https://www.dropbox.com/s/smabls57wj4pvtm/md_0_1.pdb?dl=0
i find out that all CL ions are in a strange position far away from protein
at edge of the box, well i suppose that negative Chlorine ions should be
away from each other (same charge) and close to protein which has positive
charge. which is not!
is my simulation is incorrect?
if not what cause this seemingly strange thing to happen?
Thanks in advance for any guidance


Best Regards,
Nima Soltani
---
Student of Physical Chemistry
Department of Chemistry,
Sharif University of Technology.
=
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[gmx-users] GROMACS 5 - problem with LINCS with freeze groups

[Tomek Wlodarski]

Hi,

I experience some strange behaviour and I wonder if this is a bug or I am
doing something wrong.
I am running test simulation to check freeze groups in new gromacs.
And I am getting LINCS Warnings for atoms which should be frozen...:

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max inf (between atoms 30 and 31)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 32 33   90.80.1010  23.4699  0.1010
 32 34   90.30.1010  71.2488  0.1010
[...]

my mdp file:

; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002   ; 2 femtosecond time step for integration
nsteps   = 50  ; 1ns

; OUTPUT CONTROL OPTIONS
nstxout  = 5000; save coordinates every 2 ps
nstvout  = 5000; save velocities every 2 ps
nstenergy = 5000; save energies every 2 ps
nstlog   = 5000; update log file every 2 ps
energygrps   = Protein Non-Protein
nstxtcout= 5000
xtc-grps = non-Water

; NEIGHBORSEARCHING PARAMETERS
nstlist  = 5
ns-type  = Grid
cutoff-scheme= group
pbc  = xyz
rlist= 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = pme
rcoulomb = 0.9
fourierspacing   = 0.12
ewald_rtol = 1e-5
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
optimize_fft = yes
vdw-type = Cut-off
rvdw = 1.2
energygrp_table =

; Temperature coupling
Tcoupl   = V-rescale
tc-grps  = ProteinNon-Protein
tau_t= 0.10.1
ref_t= 300300

; Freeze atoms
freezegrps   = Protein
freezedim= Y Y Y
energygrp-excl   = Protein Protein

; Pressure coupling
pcoupl   = no

;Velocity generation
gen_vel  = no
gen_temp = 300
gen_seed = -1

;Constrain all bonds
constraints = all-bonds
constraint-algorithm = Lincs
lincs_iter  = 2 ; accuracy of LINCS
lincs_order  = 6; also related to accuracy

Exactly the same system with the same mdp file I am running in Gromacs
4.6.5 and everything runs smoothly.
Any suggestions?
Thanks a lot!
Best

tomek
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Re: [gmx-users] Umbrella Sampling - Loop Motion

[Justin Lemkul]

On 11/11/14 6:21 AM, Michael Carter wrote:

Hi,

I am setting up an umbrella sampling simulation to analyse the motion of a loop 
within my protein system.

I have set it up so that the pull groups are:

1 – the loop (residues 208-14)
2 – the protein (protein)

However, when doing this my conformations which I generate in the md_pull step 
are very strained. Is this because I am also including the loop in the 2nd pull 
group (defined as protein)?



Possibly.  The normal setup would be that the two groups aren't overlapping. 
They can be part of the same molecule, but probably a more judicious choice is 
warranted here.


-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] lipid molecules are overlapping with protein molecule

[Justin Lemkul]

On 11/11/14 6:45 AM, Padmani Sandhu wrote:

Hello all,


I am trying to energy minimize a trimeric protein in DPPC bilayer but
facing problem in reaching desired lipid per area using "inflategro.pl".
After 5 or 6 steps of shrinking and energy minimization lipids molecules
start interfering with protein. I tried to increase cutt-off, but that is
also giving error during grompp.



Proper energy minimization between shrinking steps should eliminate this.

-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] Very large Max Force [Energy minimisation] in water with ions

[Justin Lemkul]

On 11/11/14 5:12 AM, Kester Wong wrote:

Dear Justin and Erik,


> Thank you for the feedback. I have also tried the following:
>
> i) separating OH- and Na+ ions
>
> ii) placing the ions much closer to water droplet
>
> iii) increase the spacing between each ions, i.e. using a larger box
>
>
> Perhaps I should try having the ions in a larger box,  then fill the box 
with
> water molecules and then redo the energy minimisation and NVT?
>

Well, like Erik said, there really isn't a smoking gun and what I'm 
observing
might be either causative or symptomatic, there's just no way to know at 
this
point.  I don't know what good any of those three options will do, because I
don't understand what you're trying to accomplish.  What was the logic of
putting a lattice of OH- and random Na+ in vacuo above a water droplet?  
What is
the goal of your simulations?


Thank you for the valuable input, the goal is to simulate the ions in water 
droplet.

Instead of having a box of water with the charged ions, I used the
water/graphene system that has been NVT equilibrated for 20ns, and placed the
ions on top of the droplet.



Adding ions within the droplet should be simple in the case of Na+, just use 
genion.  As for OH-, that's more complicated.




If adding 20 OH- and 20 Na+ proves to be problematic, is there a way to add the
ions incrementally without attracting a large force?


The OH- ions were arranged in such a way "genconf -nbox 4 5 1" as I have tried
random insertion, using gmx insert-molecules, and have found that the ions were
too close together.



Generating a grid with genconf is undoubtedly worse than random insertion; you 
have the lone pairs of the OH- nearly in contact with one another, hence massive 
repulsion with no charges close by to screen the interaction.  This is probably 
one of the central problems in your simulation.  The behavior of gmx 
insert-molecules can be changed by supplying different values to -seed or -radius.


-Justin



 From my other previous calculations, adding a cluster of H3O+ and Cl- ions
(ranging from 40 to 200 ions) on top of the water droplet worked fine with NVE
and NVT.
However, I have not been able to do so with OH- and Na+.



Regards,
Kester

-Justin

>
>
> Regards,
>
> Kester
>
> On 11/10/14 5:04 AM, Erik Marklund wrote:
> > Dear Kester,
> >
> > Hm. No obvious smoking gun as far as I can see. You could try a 
two-step minimisation where you first do one minimisation with soft-core potentials 
and then one without.
> >
>
> What's strange to me is the lattice of OH- at the top of the box and 
the sodium
> ions that are floating out in the middle of nowhere.  I don't 
understand the
> construction of this system, but having highly charged stuff in close 
contact
> and floating around in vacuum certainly looks like it could be 
trouble.
>
> -Justin
>
> > Kind regards,
> > Erik
> >
> > On 7 Nov 2014, at 05:36, Kester Wong> wrote:
> >
> >
> > Dear Erik,
> >
> > The starting structure consists of water on graphene that has 
already been energy minimised, and subsequently equilibrated (NVT) for 20ns.
> > Using that (water droplet on graphene), I added the ions for energy 
minimisation.
> > I followed a two-step minimisation:
> > i) Minimisation with no constraints (-DFLEXIBLE)
> > ii) Minimisation with constraints (SETTLES for TIPS3P water, and 
(-DCONSTRAINTS) for hydroxide)
> >
> > With the ions:
> > I have tried placing the ions box lower toward water droplet, but 
the Max Force remains large upon energy minimisation.
> >
> > The input files can be accessed here:
> > 
https://drive.google.com/folderview?id=0B7ym8d6G9-e2dG5pOFQ4SWVyZG8&usp=sharing
> >
> > The hydroxide parameter is taken from Gerrit Groenhof, based on the 
supplementary material in this paper:
> > http://dx.doi.org/10.1016/j.bpj.2014.04.062
> >
> > In short, this model was developed very similarly to the 
polarisable version of hydroxide in the SWM4-NDP force field.
> > As for sodium and graphene, the topology parameters were taken from 
CHARMM27; TIPS3P was used for the water model.
> >
> > Visualisation after the energy minimisation showed a distorted 
virtual site of the hydroxide ions, where one of the four virtual sites no longer 
conform to the constraint. So, I am guessing whether the extremely large Max Force 
originates from the force constants in the hydroxide topology?
> >
> > Thank you for your time and assistance!
> > -Kester
> > - 원본 메일 -
> > 보낸사람 : Erik Marklund>
> > 받는사람 : ">">
> > 받은날짜 : 2014년 11월 6일(목) 20:35:59

Re: [gmx-users] Error while running free energy simulation.

[Justin Lemkul]

On 11/11/14 2:12 AM, vivek sharma wrote:

Dear Users,
I am trying to replicate the free energy tutorial by Dr Justin. In my
attempt I have calculated the OPLS-AA FF parameters for my molecules of
interest using acpype. I made the system in water and 1-octanol, While
running the independent lambda simulation for both the systems, I got an
error while running the simulation for 1-octanol system whereas the
simulation for water system were successful.

Following is the error message reported in failed simulation for 1-octanol
system


Which lambda state fails?  Or is it multiple?  Does failure occur during 
equilibration or production?  If the latter, you probably just need to 
equilibrate more thoroughly.  If the former, energy-minimize more rigorously.


-Justin


--
WARNING: Listed nonbonded interaction between particles 842 and 851
at distance 427.422 which is larger than the table limit 2.200 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

-

I tried running the same system without free energy option ( free_energy
= no), which was successful. It has narrowed the reason for
error to be the free energy code.
It will be really helpful if anybody can help me in understanding the
probable reason for error and any directions for handling this error.

Pasting below the mdp options for one of the independent lambda simulation
for reference.
---
; Run control
integrator   = sd   ; Langevin dynamics
tinit= 0
dt   = 0.002
nsteps   = 250   ; 5 ns
nstcomm  = 100
; Output control
nstxout  = 500
nstvout  = 500
nstfout  = 0
nstlog   = 500
nstenergy= 500
nstxout-compressed   = 0
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme= verlet
nstlist  = 20
ns_type  = grid
pbc  = xyz
rlist= 1.2
; Electrostatics
coulombtype  = PME
rcoulomb = 1.2
; van der Waals
vdwtype  = cutoff
vdw-modifier = potential-switch
rvdw-switch  = 1.0
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps  = system
tau_t= 1.0
ref_t= 300
; Pressure coupling is on for NPT
Pcoupl   = Parrinello-Rahman
tau_p= 1.0
compressibility  = 4.5e-05
ref_p= 1.0
; Free energy control stuff
free_energy  = yes
init_lambda_state= 0
delta_lambda = 0
calc_lambda_neighbors= 1; only immediate neighboring windows
; Vectors of lambda specified here
; Each combination is an index that is retrieved from init_lambda_state for
each simulation
; init_lambda_state0123456789
  10   11   12   13   14   15   16   17   18   19   20
vdw_lambdas  = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80
0.90 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00
; We are not transforming any bonded or restrained interactions
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
; Masses are not changing (particle identities are the same at lambda = 0
and lambda = 1)
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
; Not doing simulated temperting here
temperature_lambdas  = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.0

Re: [gmx-users] How much different run (with posre.itp) from no posre.itp?

[Justin Lemkul]

On 11/11/14 12:30 AM, Batdorj Batsaikhan wrote:

Dear gmx-users,

I run 3 different conformation of a protein. I run 2 of them no posre.itp and 
another one has posre.itp. How much different these two run?



Impossible to tell.  You've got too many variables - different conformations, 
different application of restraints, as well as (presumably) different random 
velocities at the outset of each run.  Even if you could control for different 
factors, I don't know what you'd hope to learn by comparing such simulations.


-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] lipid molecules are overlapping with protein molecule

[Padmani Sandhu]

Hello all,


I am trying to energy minimize a trimeric protein in DPPC bilayer but
facing problem in reaching desired lipid per area using "inflategro.pl".
After 5 or 6 steps of shrinking and energy minimization lipids molecules
start interfering with protein. I tried to increase cutt-off, but that is
also giving error during grompp.


Thanks



Padmani,






-- 
*Padmani sandhu*
*Research Scholar,*
*Center for Computational Biology and Bioinformatics,*
*Central University of Himachal Pradesh,*
*Temporary Academic Block, Shahpur *
*Pin 176206, District Kangra,*
*Himachal Pradesh, India*
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[gmx-users] Umbrella Sampling - Loop Motion

[Michael Carter]

Hi,

I am setting up an umbrella sampling simulation to analyse the motion of a loop 
within my protein system.

I have set it up so that the pull groups are:

1 – the loop (residues 208-14)
2 – the protein (protein)

However, when doing this my conformations which I generate in the md_pull step 
are very strained. Is this because I am also including the loop in the 2nd pull 
group (defined as protein)?

Thanks,

Michael


The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
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Re: [gmx-users] Ligand is not in the same position as in PDB file

[Mark Abraham]

Hi,

Did you consult the link I provided? ;-)

Mark

On Tue, Nov 11, 2014 at 11:18 AM, neha bharti 
wrote:

> Thank you very much mark for your reply.
> I merge the protein and ligand file before starting the molecular dynamics
> simulation.
> Then I start the MD run.
> I don't how to  post-process the output. can you please tell me how to
> perform it or is there any article or tutorial available for that.
>
> Thanks and regards
> Neha Bharty
>
>
> >Hi,
>
> >Probably you are seeing normal behaviour in the presence of
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> <
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> >
> .
> >If you want to visualize the protein and ligand as a complex, you need to
> >post-process the output accordingly. mdrun doesn't know that you plan to
> >treat them as special.
>
> >Mark
>
> >On Tue, Nov 11, 2014 at 9:50 AM, neha bharti 
> >wrote:
>
> >> Hello All
> >>
> >> I am trying to perform MD for protein-ligand complex in popc lipid with
> >> charmm36 force field and also follow Justin A. Lemkul tutorial.
> >> I downloaded the pdb structure of protein and ligand complex and the
> >> separate the protein and ligand file and prepare the system.
> >>
> >> Finally I perform the MD run for 100 ns, I found that the ligand is not
> in
> >> the same place as present in PDB file of protein ligand complex.
> >>
> >> Is it necessary that the protein should be in the same position as
> present
> >> in protein ligand complex PDB file ??
> >>
> >> Is there something wrong in my work.
> >>
> >> Please Help.
> >>
> >>Thanks and regard
> --
> Gromacs Users mailing list
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Re: [gmx-users] Ligand is not in the same position as in PDB file

[neha bharti]

Thank you very much mark for your reply.
I merge the protein and ligand file before starting the molecular dynamics
simulation.
Then I start the MD run.
I don't how to  post-process the output. can you please tell me how to
perform it or is there any article or tutorial available for that.

Thanks and regards
Neha Bharty


>Hi,

>Probably you are seeing normal behaviour in the presence of
>http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

.
>If you want to visualize the protein and ligand as a complex, you need to
>post-process the output accordingly. mdrun doesn't know that you plan to
>treat them as special.

>Mark

>On Tue, Nov 11, 2014 at 9:50 AM, neha bharti 
>wrote:

>> Hello All
>>
>> I am trying to perform MD for protein-ligand complex in popc lipid with
>> charmm36 force field and also follow Justin A. Lemkul tutorial.
>> I downloaded the pdb structure of protein and ligand complex and the
>> separate the protein and ligand file and prepare the system.
>>
>> Finally I perform the MD run for 100 ns, I found that the ligand is not
in
>> the same place as present in PDB file of protein ligand complex.
>>
>> Is it necessary that the protein should be in the same position as
present
>> in protein ligand complex PDB file ??
>>
>> Is there something wrong in my work.
>>
>> Please Help.
>>
>>Thanks and regard
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Re: [gmx-users] Very large Max Force [Energy minimisation] in water with ions

[Kester Wong]

Dear Justin and Erik, > Thank you for the feedback. I have also tried the following:
>
> i) separating OH- and Na+ ions
>
> ii) placing the ions much closer to water droplet
>
> iii) increase the spacing between each ions, i.e. using a larger box
>
>
> Perhaps I should try having the ions in a larger box,  then fill the box with
> water molecules and then redo the energy minimisation and NVT?
>

Well, like Erik said, there really isn't a smoking gun and what I'm observing 
might be either causative or symptomatic, there's just no way to know at this 
point.  I don't know what good any of those three options will do, because I 
don't understand what you're trying to accomplish.  What was the logic of 
putting a lattice of OH- and random Na+ in vacuo above a water droplet?  What is 
the goal of your simulations?Thank you for the valuable input, the goal is to simulate the ions in water droplet.Instead of having a box of water with the charged ions, I used the water/graphene system that has been NVT equilibrated for 20ns, and placed the ions on top of the droplet.If adding 20 OH- and 20 Na+ proves to be problematic, is there a way to add the ions incrementally without attracting a large force?The OH- ions were arranged in such a way "genconf -nbox 4 5 1" as I have tried random insertion, using gmx insert-molecules, and have found that the ions were too close together.From my other previous calculations, adding a cluster of H3O+ and Cl- ions (ranging from 40 to 200 ions) on top of the water droplet worked fine with NVE and NVT.However, I have not been able to do so with OH- and Na+.Regards,Kester
-Justin

>
>
> Regards,
>
> Kester
>
> On 11/10/14 5:04 AM, Erik Marklund wrote:
> > Dear Kester,
> >
> > Hm. No obvious smoking gun as far as I can see. You could try a two-step minimisation where you first do one minimisation with soft-core potentials and then one without.
> >
>
> What's strange to me is the lattice of OH- at the top of the box and the sodium
> ions that are floating out in the middle of nowhere.  I don't understand the
> construction of this system, but having highly charged stuff in close contact
> and floating around in vacuum certainly looks like it could be trouble.
>
> -Justin
>
> > Kind regards,
> > Erik
> >
> > On 7 Nov 2014, at 05:36, Kester Wong> wrote:
> >
> >
> > Dear Erik,
> >
> > The starting structure consists of water on graphene that has already been energy minimised, and subsequently equilibrated (NVT) for 20ns.
> > Using that (water droplet on graphene), I added the ions for energy minimisation.
> > I followed a two-step minimisation:
> > i) Minimisation with no constraints (-DFLEXIBLE)
> > ii) Minimisation with constraints (SETTLES for TIPS3P water, and (-DCONSTRAINTS) for hydroxide)
> >
> > With the ions:
> > I have tried placing the ions box lower toward water droplet, but the Max Force remains large upon energy minimisation.
> >
> > The input files can be accessed here:
> > https://drive.google.com/folderview?id=0B7ym8d6G9-e2dG5pOFQ4SWVyZG8&usp=sharing
> >
> > The hydroxide parameter is taken from Gerrit Groenhof, based on the supplementary material in this paper:
> > http://dx.doi.org/10.1016/j.bpj.2014.04.062
> >
> > In short, this model was developed very similarly to the polarisable version of hydroxide in the SWM4-NDP force field.
> > As for sodium and graphene, the topology parameters were taken from CHARMM27; TIPS3P was used for the water model.
> >
> > Visualisation after the energy minimisation showed a distorted virtual site of the hydroxide ions, where one of the four virtual sites no longer conform to the constraint. So, I am guessing whether the extremely large Max Force originates from the force constants in the hydroxide topology?
> >
> > Thank you for your time and assistance!
> > -Kester
> > - 원본 메일 -
> > 보낸사람 : Erik Marklund>
> > 받는사람 : ">">
> > 받은날짜 : 2014년 11월 6일(목) 20:35:59
> > 제목 : Re: [gmx-users] Very large Max Force [Energy minimisation] in water with ions
> >
> > Dear Kester,
> >
> > The potential energy is highly positive in the first case and the force is enormous in the second case, so no wonder that they blow up. How did you prepare these systems?
> >
> > Kind regards,
> > Erik
> >
> > Erik Marklund, PhD
> > Postdoctoral Research Fellow, Fulford JRF
> >
> > Department of Chemistry
> > Physical & Theoretical Chemistry Laboratory
> > University of Oxford
> > South Parks Road
> > Oxford
> > OX1 3QZ
> >
> > On 6 Nov 2014, at 04:31, Kester Wong > wrote:
> >
> >
> > Dear all,
> >
> > I have been trying to energy minimise ~1980 water (tips3p) molecules with 20 OH- anions (

Re: [gmx-users] energy minimization of protein taken from PDB

[Mark Abraham]

Hi,

That value may indicate that the ligand is not horribly out of place,
because the total energy is negative. Showing a favourable binding
interaction is a different matter, for which this is just the tiniest first
step.

Mark

On Tue, Nov 11, 2014 at 9:04 AM, md kashif 
wrote:

> Dear Dr. Justin Lemkul
> Thanks for your kind suggestion,  I have energy minimized my protein taken
> from PDB. It gives result as  -1.5248922e+06. Taking the energy minimized
> protein generated in .gro file file and docking it with ligand and doining
> energy minimization again, it gives result  as  -1.0504211e+06.
> Is this value correct? Is my ligand showing interaction and bound to my
> protein.  Please help.
>
>
> Thanking You
> --
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Re: [gmx-users] Ligand is not in the same position as in PDB file

[Mark Abraham]

Hi,

Probably you are seeing normal behaviour in the presence of
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions.
If you want to visualize the protein and ligand as a complex, you need to
post-process the output accordingly. mdrun doesn't know that you plan to
treat them as special.

Mark

On Tue, Nov 11, 2014 at 9:50 AM, neha bharti 
wrote:

> Hello All
>
> I am trying to perform MD for protein-ligand complex in popc lipid with
> charmm36 force field and also follow Justin A. Lemkul tutorial.
> I downloaded the pdb structure of protein and ligand complex and the
> separate the protein and ligand file and prepare the system.
>
> Finally I perform the MD run for 100 ns, I found that the ligand is not in
> the same place as present in PDB file of protein ligand complex.
>
> Is it necessary that the protein should be in the same position as present
> in protein ligand complex PDB file ??
>
> Is there something wrong in my work.
>
> Please Help.
>
> Thanks and regards
>
> Neha Bharty
> --
> Gromacs Users mailing list
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[gmx-users] Ligand is not in the same position as in PDB file

[neha bharti]

Hello All

I am trying to perform MD for protein-ligand complex in popc lipid with
charmm36 force field and also follow Justin A. Lemkul tutorial.
I downloaded the pdb structure of protein and ligand complex and the
separate the protein and ligand file and prepare the system.

Finally I perform the MD run for 100 ns, I found that the ligand is not in
the same place as present in PDB file of protein ligand complex.

Is it necessary that the protein should be in the same position as present
in protein ligand complex PDB file ??

Is there something wrong in my work.

Please Help.

Thanks and regards

Neha Bharty
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[gmx-users] energy minimization of protein taken from PDB

[md kashif]

Dear Dr. Justin Lemkul
Thanks for your kind suggestion,  I have energy minimized my protein taken
from PDB. It gives result as  -1.5248922e+06. Taking the energy minimized
protein generated in .gro file file and docking it with ligand and doining
energy minimization again, it gives result  as  -1.0504211e+06.
Is this value correct? Is my ligand showing interaction and bound to my
protein.  Please help.


Thanking You
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