Re: [gmx-users] membed in mdrun VERSION 5.0.4

[Nash, Anthony]

Many thanks Justin, that’s solved it.

The simulation is now running, reporting that 8 POPC molecules and 12 SOL
molecules have been removed. However, I have a bit of a problem. I don’t
seem to be able to get the -membed option working on a parallel
installation of gromacs, only serial. I assume parallel isn’t supported?

Secondly, with my .tpr file very different from my running .trr (due to
removed molecules), I don’t know of a way of pulling out a single frame
from the trajectory to see how the simulation is progressing. (I would
have just taken the first frame as a .gro, downloaded the latest .trr, and
thrown them both into VMD). Any thoughts?

Many thanks
Anthony 




On 06/01/2016 19:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Justin Lemkul"
 wrote:

>
>
>On 1/6/16 2:00 PM, Nash, Anthony wrote:
>> Hi all,
>>
>> I thought I would try using the -membed option of mdrun to insert a
>> helical dimer into a lipid bilayer. I¹ve followed the .mdp instructions
>>on
>> g_membed to generate my required .tpr file. Upon calling grommp I get:
>>
>> ERROR 1 [file membed_NPT.mdp]:
>>Energy group exclusions are not (yet) implemented for the Verlet
>>scheme
>>
>>
>> My input file can be seen below. If seems as though the Integrator is
>>the
>> issue, even though I¹ve picked the correct one. Is a place holder
>>feature?
>>
>
>It's not the integrator that's the problem.  It is, as the error states,
>the use 
>of the Verlet cutoff scheme.  Presumably "cutoff-scheme = group" would
>circumvent this issue.
>
>-Justin
>
>> Many thanks
>> Anthony
>>
>> integrator = md
>> energygrps = Protein
>> freezegrps = Protein
>> freezedim = Y Y Y
>> energygrp_excl = Protein Protein
>>
>>
>> nsteps  = 500   ; 2 * 50 = 1000 ps (2 ns)
>> dt  = 0.002 ; 2 fs
>> nstxout = 1 ; save coordinates every 0.2 ps
>> nstvout = 1 ; save velocities every 0.2 ps
>> nstenergy   = 1 ; save energies every 0.2 ps
>> nstlog  = 1 ; update log file every 0.2 ps
>>
>> continuation= yes   ; Restarting after NVT
>> constraint_algorithm = lincs; holonomic constraints
>> constraints = all-bonds ; all bonds (even heavy atom-H
>> bonds) constrained
>> lincs_iter  = 1 ; accuracy of LINCS
>> lincs_order = 4 ; also related to accuracy
>>
>> ns_type = grid  ; search neighboring grid cels
>> nstlist = 5 ; 10 fs
>> rlist   = 1.0   ; short-range neighborlist cutoff (in
>>nm)
>> rcoulomb= 1.0   ; short-range electrostatic cutoff (in
>>nm)
>> rvdw= 1.0   ; short-range van der Waals cutoff (in
>>nm)
>>
>> coulombtype = PME   ; Particle Mesh Ewald for long-range
>> electrostatics
>> pme_order   = 4 ; cubic interpolation
>> fourierspacing  = 0.16  ; grid spacing for FFT
>>
>> tcoupl  = Berendsen   ;Nose-Hoover  ; More
>> accurate thermostat
>> tc-grps = Protein  POPC SOL ; three coupling groups - more
>> accurate
>> tau_t   = 0.5   0.5 0.5 ; time constant, in ps
>> ref_t   = 310   310 310 ; reference temperature,
>> one for each group, in K
>>
>> pcoupl  = Parrinello-Rahman ; Pressure coupling on in
>>NPT
>> pcoupltype  = semiisotropic ; uniform scaling of x-y box
>> vectors, independent z
>> tau_p   = 5.0   ; time constant, in ps
>> ref_p   = 1.0   1.0 ; reference pressure,
>>x-y,
>> z (in bar)
>> compressibility = 4.5e-54.5e-5  ; isothermal compressibility,
>> bar^-1
>>
>> pbc = xyz   ; 3-D PBC
>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>> gen_vel = no; Velocity generation is off
>> nstcomm = 1
>> comm-mode   = Linear
>> comm-grps   = POPC_Protein SOL
>> refcoord_scaling = com
>>
>>
>
>-- 
>==
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalem...@outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==
>-- 
>Gromacs Users mailing list
>
>* Please search the archive at
>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>posting!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>* For (un)subscribe requests visit
>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>send a mail to 

[gmx-users] Serine phosphorylation

[Simone Bolognini]

Hi everyone,
I need to run some MD simulations with a protein where a particular serine
should be phosphorylated. Since in the original pdb the serine is actually
not, I guess I should modify something 'by hand'. I'm going to use
AMBER-ILDN ff. Can anyone of you tell me what should I do? My first guess
was to generate the topology and then directly substitute my serine with
the phosphorylated one (looking for the AMBER-ILDN parameters), but
sincerely I don't know if this is the correct way to proceed.

Thanks a lot for your support!
Simone
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Generating topology of 3b68.ent

[Simone Bolognini]

This was very useful thanks!! Actually I realized that Swiss Pdb Viewer
automatically tries to reconstruct the missing atom positions, so that now
I have the topology.

Thanks a lot!
Simone

Il giorno ven 8 gen 2016 alle ore 00:02 Peter Stern <
peter.st...@weizmann.ac.il> ha scritto:

> Look for any "MISSING ATOMS" in the pdb file (in the REMARKS).
> Look at the coordinates given for the LYS in question and check if there
> are coordinates for the CG.
>
> Experimental data isn't "perfect."  PDB entries have missing residues and
> missing atoms all the time because they couldn't be resolved.
>
> "Detective work" is over-glamorizing it.
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Simone
> Bolognini
> Sent: Thursday, January 07, 2016 8:37 PM
> To: gmx-us...@gromacs.org
> Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Generating topology of 3b68.ent
>
> Hi Mark,
> Thank you for your fast aswer. However, I don't quite get what you mean by
> "detective work". What should I exactly look for?
> Il 07/gen/2016 19:25, "Mark Abraham"  ha
> scritto:
>
> > Hi,
> >
> > It could just be missing from the experimental data. You'll need to do
> > some detective work about that pdb entry.
> >
> > Mark
> >
> > On Thu, 7 Jan 2016 19:05 Simone Bolognini 
> > wrote:
> >
> > > Good evening everyone,
> > > I was trying to generate the topology of the ligand binding domain
> > > of the human androgen receptor (3B68) with pdb2gmx using pdb2gmx -f
> > > 3b68.ent -o ar.gro -p ar.top -ignh using the AMBER-ILDN ff and
> > > implict solvent (therefore typing 6 and 6
> > again
> > > on gromacs v. 4.6.5) and it throws me the following error:
> > >
> > > Fatal error:
> > > Residue 177 named LYS of a molecule in the input file was mapped to
> > > an entry in the topology database, but the atom CG used in that
> > > entry is not found in the input file. Perhaps your atom and/or
> > > residue naming needs to be fixed.
> > >
> > > What am I doing wrong? You can find the .ent here:
> > > http://www.rcsb.org/pdb/explore/explore.do?structureId=3b68
> > > Thank you very much for your support!!
> > >
> > > Simone
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > or send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Correct method to do Cartesian PCA

[Antonio Baptista]

On Fri, 8 Jan 2016, Bin Liu wrote:


Hi Tsjerk,

I replicated their settings in their papers. The system size I used is
larger than what they had. Could you elaborate on the reference used for
fitting? Thank you so much.


About the importance of the reference structure used for fitting in 
Cartesian PCA, you may want to look at this: 
http://dx.doi.org/10.1021/jp902991u


Best,

--
Antonio M. Baptista
Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
Av. da Republica - EAN, 2780-157 Oeiras, Portugal
phone: +351-214469619 email: bapti...@itqb.unl.pt
fax:   +351-214411277 WWW:   http://www.itqb.unl.pt/~baptista
--




Cheers,

Bin

Message: 3
Date: Fri, 8 Jan 2016 18:29:26 +0100
From: Tsjerk Wassenaar 
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Correct method to do Cartesian PCA
Message-ID:
   
Content-Type: text/plain; charset=UTF-8

Hi Bin,

Did you use the same force field, simulation length, other parameters? The
system size might play a role too. And for trialanine the reference used
for fitting may matter too. But first check all the other
similarities/differences.

Cheers,

Tsjerk
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.


--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Correct method to do Cartesian PCA

[Bin Liu]

Hi Tsjerk,

I replicated their settings in their papers. The system size I used is
larger than what they had. Could you elaborate on the reference used for
fitting? Thank you so much.

Cheers,

Bin

Message: 3
Date: Fri, 8 Jan 2016 18:29:26 +0100
From: Tsjerk Wassenaar 
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Correct method to do Cartesian PCA
Message-ID:

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

Hi Bin,

Did you use the same force field, simulation length, other parameters? The
system size might play a role too. And for trialanine the reference used
for fitting may matter too. But first check all the other
similarities/differences.

Cheers,

Tsjerk
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] ionic liquids - viscosity using green kubo relation

[shanmuga sundaram]

Hello all,


I am trying to find viscosity using green kubo relation for Ionic Liquids.
I got pressure tensor values (pxx, pyy, pzz, ….) from energy file .edr. How
to get stress autocorrelation function (SACF) from pressure autocorrelation
function in MD simulations? Also how to change ACF windows (10, 50, 200ps)
in getting autocorrelation function from gromacs (usually from g_analyze
tool)?


regards,

shanu
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Problem in using pdb2gmx to generate top file

[张敏华]

Hi everyone, I encountered a problem when I using pdb2gmx to convert a pdb file 
into gro and top file. The system give me a fatal error message as following:
 
Fatal error:
Residue 145 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

But the 145 residue is LEU actually, and the sidechain of this residue is OK, I 
replaced this residue with ALA, ARG or LYS but the error message remains. So 
does anyone know the cause and help me to solve this ?

Thanks




-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] MSD calculation

[??????]

Hi GMX users:

I did a simulation of a bilayer, and I would like to calculate the diffusion 
coefficent of lipids by g_msd command.

I used the following command:
g_msd -s *.tpr -f *.xtc -n index.ndx -beginfit xx -endfit xx -trestart xx -o 
msd.xvg
I have 144 lipids in one leaflet. I am wondering what is the msd plot I got. To 
my understanding, the MSD was calculated based on the move of the center of 
mass of each lipid molecular, right? Or the MSD was calculated based on the 
move of all of the atoms I selected?
There is an option -ngroup, what does this option mean?
Thanks very much, I am really appreciate for any help. 

Cheers, 
RXG
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] membed in mdrun VERSION 5.0.4

[Nash, Anthony]

Justin and Mark, many thanks for your help.

With regards to the parallelization, when did parallel membed become
supported? I¹ve just tried on 5.0.4 and I¹m getting the response:

Reading file membed_NPT_B.tpr, VERSION 5.0.4 (double precision)

---
Program mdrun_mpi_d, VERSION 5.0.4
Source code file: 
/dev/shm/tmp.3LEFQsSzrx/gromacs-5.0.4/src/programs/mdrun/membed.c, line:
1056


Input error or input inconsistency:
Sorry, parallel g_membed is not yet fully functional.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Error on rank 0, will try to stop all ranks
Halting parallel program mdrun_mpi_d on CPU 0 out of 2



Oh course, I understand this could be answered by installing the latest
version, but I¹m ruling out anything I¹ve done wrong before asking central
IT to put up a test module.

Thanks for the help
Anthony 





On 08/01/2016 13:24, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Mark Abraham"  wrote:

>Hi,
>
>The current implementation of membed is quite sane and should support all
>kinds of parallelization. (It is difficult to say much that is nice about
>the first implementation, though!)
>
>gmx trjconv and convert-tpr are good for making subsets from well chosen
>index groups.
>
>Mark
>
>On Fri, 8 Jan 2016 13:35 Justin Lemkul  wrote:
>
>>
>>
>> On 1/8/16 3:38 AM, Nash, Anthony wrote:
>> > Many thanks Justin, that¹s solved it.
>> >
>> > The simulation is now running, reporting that 8 POPC molecules and 12
>>SOL
>> > molecules have been removed. However, I have a bit of a problem. I
>>don¹t
>> > seem to be able to get the -membed option working on a parallel
>> > installation of gromacs, only serial. I assume parallel isn¹t
>>supported?
>> >
>>
>> No idea, but the -membed incorporation into mdrun is currently a very
>>big
>> hack
>> to make it work, so you should expect limited support for features.
>>
>> > Secondly, with my .tpr file very different from my running .trr (due
>>to
>> > removed molecules), I don¹t know of a way of pulling out a single
>>frame
>> > from the trajectory to see how the simulation is progressing. (I would
>> > have just taken the first frame as a .gro, downloaded the latest .trr,
>> and
>> > thrown them both into VMD). Any thoughts?
>> >
>>
>> Does the program report which residues were removed?  If so, you can
>>just
>> remove
>> those from the coordinate file you had before.  Otherwise, no, probably
>> not.
>> Like I said, big hack to get it working in the present version.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>-- 
>Gromacs Users mailing list
>
>* Please search the archive at
>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>posting!
>
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>* For (un)subscribe requests visit
>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>send a mail to gmx-users-requ...@gromacs.org.

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] membed in mdrun VERSION 5.0.4

[Justin Lemkul]

On 1/8/16 3:38 AM, Nash, Anthony wrote:
> Many thanks Justin, that’s solved it.
> 
> The simulation is now running, reporting that 8 POPC molecules and 12 SOL
> molecules have been removed. However, I have a bit of a problem. I don’t
> seem to be able to get the -membed option working on a parallel
> installation of gromacs, only serial. I assume parallel isn’t supported?
> 

No idea, but the -membed incorporation into mdrun is currently a very big hack
to make it work, so you should expect limited support for features.

> Secondly, with my .tpr file very different from my running .trr (due to
> removed molecules), I don’t know of a way of pulling out a single frame
> from the trajectory to see how the simulation is progressing. (I would
> have just taken the first frame as a .gro, downloaded the latest .trr, and
> thrown them both into VMD). Any thoughts?
> 

Does the program report which residues were removed?  If so, you can just remove
those from the coordinate file you had before.  Otherwise, no, probably not.
Like I said, big hack to get it working in the present version.

-Justin

-- 
==

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

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

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

==
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] How to get a compressed pull force output from SMD simulation ?

[Justin Lemkul]

On 1/8/16 12:00 AM, Agnivo Gosai wrote:

Dear Users,

I use GROMACS to do SMD simulation. I have the pullf.xvg file , but it is
very large. I also have the smd.xtc file. I have used it to calculate the
COM separation distance between the two pulled groups.

I want to plot force vs COM separation.

Can I calculate the pull force from the .xtc file so that the pull force
and the COM separation are of same vector lengths? or do I need to add
something to my .mdp file to be able to do  it ? Like , nstfout ??

I did not download the trr file from the cluster as it is very huge !

Kindly help please.



Pulling forces are printed to pullf.xvg at an interval of pull-nstfout in the 
.mdp file.


-Justin

--
==

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

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

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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] membed in mdrun VERSION 5.0.4

[Mark Abraham]

Hi,

The current implementation of membed is quite sane and should support all
kinds of parallelization. (It is difficult to say much that is nice about
the first implementation, though!)

gmx trjconv and convert-tpr are good for making subsets from well chosen
index groups.

Mark

On Fri, 8 Jan 2016 13:35 Justin Lemkul  wrote:

>
>
> On 1/8/16 3:38 AM, Nash, Anthony wrote:
> > Many thanks Justin, that’s solved it.
> >
> > The simulation is now running, reporting that 8 POPC molecules and 12 SOL
> > molecules have been removed. However, I have a bit of a problem. I don’t
> > seem to be able to get the -membed option working on a parallel
> > installation of gromacs, only serial. I assume parallel isn’t supported?
> >
>
> No idea, but the -membed incorporation into mdrun is currently a very big
> hack
> to make it work, so you should expect limited support for features.
>
> > Secondly, with my .tpr file very different from my running .trr (due to
> > removed molecules), I don’t know of a way of pulling out a single frame
> > from the trajectory to see how the simulation is progressing. (I would
> > have just taken the first frame as a .gro, downloaded the latest .trr,
> and
> > thrown them both into VMD). Any thoughts?
> >
>
> Does the program report which residues were removed?  If so, you can just
> remove
> those from the coordinate file you had before.  Otherwise, no, probably
> not.
> Like I said, big hack to get it working in the present version.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Problem in using pdb2gmx to generate top file

[Justin Lemkul]

On 1/8/16 5:46 AM, 张敏华 wrote:

Hi everyone, I encountered a problem when I using pdb2gmx to convert a pdb file 
into gro and top file. The system give me a fatal error message as following:

Fatal error:
Residue 145 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

But the 145 residue is LEU actually, and the sidechain of this residue is OK, I 
replaced this residue with ALA, ARG or LYS but the error message remains. So 
does anyone know the cause and help me to solve this ?



pdb2gmx uses its own internal residue numbering.  You must have a lysine 
somewhere with an incomplete side chain (a very common problem).  You'll need to 
fix the structure using e.g. SwissPDBViewer or some other modeling software 
before running the structure through pdb2gmx.


-Justin

--
==

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

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

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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Error while running mdrun with rerun option for LIE calculation

[Justin Lemkul]

On 1/8/16 12:50 AM, shagun krishna wrote:

Hiii Justin,

Thank you very much for your help. After changing my settings according to
your suggestions I am not getting the previous errors. :) The grompp
command ran successfully, but when I am evoking the mdrun using rerun
option I am getting a fatal error. Please have a look at my terminal
window. And let me know how to solve this. What I guess that probably I
should increase my box size. My ligand has almost 55 atom.



You're post-processing an existing system; you can't increase the box size and 
make anything work.  The error is related to domain decomposition, which you 
don't need during a rerun anyway, so just do the rerun on a single core (or 
maybe via OpenMP, but I don't know if that works).  Just avoid MPI, which 
triggers DD.


-Justin


cbb@cbb-Precision-T1700:~/Desktop/md_ligand_RJC02836$ grompp -f
md_SOL_rerun.mdp -c equil.gro -o md_sol_rerun.tpr
  :-)  G  R  O  M  A  C  S  (-:

 :-)  VERSION 4.6.5  (-:

   Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16#

NOTE 1 [file md_SOL_rerun.mdp]:
   nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
   nstcomm to nstcalcenergy

Generated 168 of the 1653 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'M_R'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...

NOTE 2 [file topol.top]:
   The largest charge group contains 11 atoms.
   Since atoms only see each other when the centers of geometry of the charge
   groups they belong to are within the cut-off distance, too large charge
   groups can lead to serious cut-off artifacts.
   For efficiency and accuracy, charge group should consist of a few atoms.
   For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

Analysing residue names:
There are: 1  Other residues
There are:   859  Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group M_R is 106.94
Number of degrees of freedom in T-Coupling group SOL is 5151.06
Largest charge group radii for Van der Waals: 0.370, 0.293 nm
Largest charge group radii for Coulomb:   0.370, 0.307 nm

NOTE 3 [file md_SOL_rerun.mdp]:
   The sum of the two largest charge group radii (0.676770) is larger than
   rlistlong (1.40) - rcoulomb (0.90).
   With exact cut-offs, better performance can be obtained with
   cutoff-scheme = Verlet, because it does not use charge groups at all.

This run will generate roughly 199 Mb of data

There were 3 notes

Back Off! I just backed up md_sol_rerun.tpr to ./#md_sol_rerun.tpr.2#

gcq#139: "We All Get the Flu, We All Get Aids" (LIVE)

cbb@cbb-Precision-T1700:~/Desktop/md_ligand_RJC02836$ mdrun -s
md_sol_rerun.tpr -rerun md_sol.xtc
  :-)  G  R  O  M  A  C  S  (-:

 Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm

 :-)  VERSION 4.6.5  (-:

 :-)  mdrun  (-:
Back Off! I just backed up md.log to ./#md.log.2#
Reading file md_sol_rerun.tpr, VERSION 4.6.5 (single precision)
Using 4 MPI threads
Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this machine,
which is better)

Back Off! I just backed up traj.trr to ./#traj.trr.2#

Back Off! I just backed up ener.edr to ./#ener.edr.2#
starting md rerun 'M_R in water', reading coordinates from input trajectory
'md_sol.xtc'

Reading frame   0 time0.000
WARNING: Some frames do not contain velocities.
  Ekin, temperature and pressure are incorrect,
  the virial will be incorrect when constraints are present.

Reading frame 140 time  280.000
DD cell 0 0 0: Neighboring cells do not have atoms: 45

DD cell 2 0 0: Neighboring cells do not have atoms: 32

---
Program mdrun, VERSION 4.6.5
Source code file: /build/buildd/gromacs-4.6.5/src/mdlib/domdec_con.c, line:
722

Fatal error:
DD cell 0 0 0 could only obtain 11 of the 12 atoms that are connected via
constraints from the neighboring cells. This probably means your constraint
lengths are too long compared to the domain decomposition cell size.
Decrease the number of domain decomposition grid cells or lincs-order.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Thanks a ton...I am really very thankful to you... :)

Best regards,

Shagun



--
==

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 

Re: [gmx-users] Correct method to do Cartesian PCA

[Bin Liu]

Hi Tsjerk,

I used trjconv -pbc and trjconv -nojump to remove PBC and jump across the
boundary before I applied  g_covar. This paper is about dPCA indeed. But it
also contains the author's results on cPCA. Thank you for your help.

Regards,

Bin



Message: 6
Date: Thu, 7 Jan 2016 23:38:44 +0100
From: Tsjerk Wassenaar 
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Correct method to do Cartesian PCA
Message-ID:

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

Hi Bin,

The procedure is correct, provided you ensured that the input trajectory
did not have PBC jumps. But the paper you refer to is on dihedral angle
PCA...

Cheers,

Tsjerk
On Jan 7, 2016 23:06, "Bin Liu"  wrote:

> Hi All,
>
> I am trying to reproduce the Cartesian PCA results for ALA3 in water by
> Altis et al. (Fig.2 of Dihedral angle principal component analysis of
> molecular dynamics simulations.   http://dx.doi.org/10.1063/1.2746330 )
> It is probably the most well-known PCA analysis results. I created a
system
> as they suggested and got a 100 ns trajectory (after an equilibration
> stage) for applying PCA.
>
> GROMOS96 43a1
> SPC water
> 300 K, 1 atm
> PME
> cutoff 1.0 nm
> Box larger than they did, 2100~ waters
>
> As all the PCA tutorials indicate, applying Cartesian PCA can be as simple
> as two commands, g_covar and g_anaeig. However with all my effort of
trying
> all the combinations of arguments I can think of, I still can't reproduce
> the literature results. Here I humbly request help from experienced users
> who have applied PCA before.
>
> The following is my approach. Suppose I have a .tpr file
*npt_pr_100ns.tpr*
> and a .trr file *npt_pr_100ns.trr*
>
> *g_covar -s npt_pr_100ns.tpr -f npt_pr_100ns.trr -o eigenval.xvg -v
> eigenvec.trr -av average.pdb -l covar.log*
> Choose a group for the least squares fit
> Group 0 ( System) has  6518 elements
> Group 1 (Protein) has22 elements
> Group 2 (  Protein-H) has16 elements
> ...
> Select a group: 1
> Selected 1: 'Protein'
>
> Choose a group for the covariance analysis
> Group 0 ( System) has  6518 elements
> Group 1 (Protein) has22 elements
> Group 2 (  Protein-H) has16 elements
> ...
> Select a group: 1
> Selected 1: 'Protein'
>
> *g_anaeig -v eigenvec.trr
> -f npt_pr_100ns.trr -s npt_pr_100ns.tpr -2d 2dproj.xvg -first 1 -last 2*
>
> Select the index group that was used for the least squares fit in g_covar
> Group 0 ( System) has  6518 elements
> Group 1 (Protein) has22 elements
> Group 2 (  Protein-H) has16 elements
> ...
> Select a group: 1
> Selected 1: 'Protein'
>
> Select an index group of 22 elements that corresponds to the eigenvectors
> Group 0 ( System) has  6518 elements
> Group 1 (Protein) has22 elements
> Group 2 (  Protein-H) has16 elements
> ...
> Select a group: 1
> Selected 1: 'Protein'
>
> Is there anything I did incorrectly?  Another question: is -mwa argument
> which turns on mass weighting for g_covar necessary?  Thank you very much.
>
> Best Regards,
>
> Bin
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Correct method to do Cartesian PCA

[Tsjerk Wassenaar]

Hi Bin,

Did you use the same force field, simulation length, other parameters? The
system size might play a role too. And for trialanine the reference used
for fitting may matter too. But first check all the other
similarities/differences.

Cheers,

Tsjerk
On Jan 8, 2016 16:35, "Bin Liu"  wrote:

> Hi Tsjerk,
>
> I used trjconv -pbc and trjconv -nojump to remove PBC and jump across the
> boundary before I applied  g_covar. This paper is about dPCA indeed. But it
> also contains the author's results on cPCA. Thank you for your help.
>
> Regards,
>
> Bin
>
>
>
> Message: 6
> Date: Thu, 7 Jan 2016 23:38:44 +0100
> From: Tsjerk Wassenaar 
> To: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] Correct method to do Cartesian PCA
> Message-ID:
> <
> cabze1shyqdeg4sexss5qtjcy7qfg8s+2jsh3pmchufh4xnr...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Bin,
>
> The procedure is correct, provided you ensured that the input trajectory
> did not have PBC jumps. But the paper you refer to is on dihedral angle
> PCA...
>
> Cheers,
>
> Tsjerk
> On Jan 7, 2016 23:06, "Bin Liu"  wrote:
>
> > Hi All,
> >
> > I am trying to reproduce the Cartesian PCA results for ALA3 in water by
> > Altis et al. (Fig.2 of Dihedral angle principal component analysis of
> > molecular dynamics simulations.   http://dx.doi.org/10.1063/1.2746330 )
> > It is probably the most well-known PCA analysis results. I created a
> system
> > as they suggested and got a 100 ns trajectory (after an equilibration
> > stage) for applying PCA.
> >
> > GROMOS96 43a1
> > SPC water
> > 300 K, 1 atm
> > PME
> > cutoff 1.0 nm
> > Box larger than they did, 2100~ waters
> >
> > As all the PCA tutorials indicate, applying Cartesian PCA can be as
> simple
> > as two commands, g_covar and g_anaeig. However with all my effort of
> trying
> > all the combinations of arguments I can think of, I still can't reproduce
> > the literature results. Here I humbly request help from experienced users
> > who have applied PCA before.
> >
> > The following is my approach. Suppose I have a .tpr file
> *npt_pr_100ns.tpr*
> > and a .trr file *npt_pr_100ns.trr*
> >
> > *g_covar -s npt_pr_100ns.tpr -f npt_pr_100ns.trr -o eigenval.xvg -v
> > eigenvec.trr -av average.pdb -l covar.log*
> > Choose a group for the least squares fit
> > Group 0 ( System) has  6518 elements
> > Group 1 (Protein) has22 elements
> > Group 2 (  Protein-H) has16 elements
> > ...
> > Select a group: 1
> > Selected 1: 'Protein'
> >
> > Choose a group for the covariance analysis
> > Group 0 ( System) has  6518 elements
> > Group 1 (Protein) has22 elements
> > Group 2 (  Protein-H) has16 elements
> > ...
> > Select a group: 1
> > Selected 1: 'Protein'
> >
> > *g_anaeig -v eigenvec.trr
> > -f npt_pr_100ns.trr -s npt_pr_100ns.tpr -2d 2dproj.xvg -first 1 -last 2*
> >
> > Select the index group that was used for the least squares fit in g_covar
> > Group 0 ( System) has  6518 elements
> > Group 1 (Protein) has22 elements
> > Group 2 (  Protein-H) has16 elements
> > ...
> > Select a group: 1
> > Selected 1: 'Protein'
> >
> > Select an index group of 22 elements that corresponds to the eigenvectors
> > Group 0 ( System) has  6518 elements
> > Group 1 (Protein) has22 elements
> > Group 2 (  Protein-H) has16 elements
> > ...
> > Select a group: 1
> > Selected 1: 'Protein'
> >
> > Is there anything I did incorrectly?  Another question: is -mwa argument
> > which turns on mass weighting for g_covar necessary?  Thank you very
> much.
> >
> > Best Regards,
> >
> > Bin
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Error while running mdrun with rerun option for LIE calculation

[shagun krishna]

Dear Justin,

Thanks a lot. I have successfully completed mdrun with -rerun option. I
have ran the mdrun command on the original mdrun.xtc using new .mdp
settings without PME, and the result was stored in new .edr file. This new
.edr file was then subjected to g_energy to obtain the values of LJ-17 and
Coulomb-14. Hope we have to calculate this only not the LJ-(SR) or
Coulomb-(SR) ?

>>>  mdrun -s md_sol_rerun_LLP.tpr (ORIGINAL tpr obtained from Ligand
Simulation in water) -rerun md2_LLP.xtc ( ORIGINAL ,xtc obtained from
Ligand Simulation in water) -x after_rerun_trial4.xtc (OUTPUT) -e
after_rerun_trial4.edr (OUTPUT)

After that I calculated value of Elj and Eqq from g_energy module by
passing these output to g_energy:

 g_energy -f after_rerun_trial4.edr -o after_rerun_trial4_C-14.xvg

g_energy -f after_rerun_trial4.edr -o after_rerun_trial4_LJ-14.xvg

I got Elj= 271.04 and Eqq=-149.214. Then these values were passed to g_lie
module to get the Delta G for unbound ligand.

 g_lie -f after_rerun_trial4.edr -b 7000 -e 1 -Elj 271.04 -Eqq
-149.214 -ligand M_R -o lie_ligand.xvg


I am taking last 3000ps of my simulation for calculating energy. Is it good
or should I calculate it from 0 to 1ps.

After passing these values to g_lie I am getting DGbind = -8.956 (214.311).
In g_lie module we will give the original .edr file or that we have
obtained after rerun. However, I have used the .edr obtained with rerun
option. The values of Clj and Cqq were taken as default (0.181 and 0.5
respectively). I want to know that do we also need to calculate the values
of Clj and Cqq ???
Thanks once again in advance :)

Best regards,

Shagun

On Fri, Jan 8, 2016 at 6:06 PM, Justin Lemkul  wrote:

>
>
> On 1/8/16 12:50 AM, shagun krishna wrote:
>
>> Hiii Justin,
>>
>> Thank you very much for your help. After changing my settings according to
>> your suggestions I am not getting the previous errors. :) The grompp
>> command ran successfully, but when I am evoking the mdrun using rerun
>> option I am getting a fatal error. Please have a look at my terminal
>> window. And let me know how to solve this. What I guess that probably I
>> should increase my box size. My ligand has almost 55 atom.
>>
>>
> You're post-processing an existing system; you can't increase the box size
> and make anything work.  The error is related to domain decomposition,
> which you don't need during a rerun anyway, so just do the rerun on a
> single core (or maybe via OpenMP, but I don't know if that works).  Just
> avoid MPI, which triggers DD.
>
> -Justin
>
>
> cbb@cbb-Precision-T1700:~/Desktop/md_ligand_RJC02836$ grompp -f
>> md_SOL_rerun.mdp -c equil.gro -o md_sol_rerun.tpr
>>   :-)  G  R  O  M  A  C  S  (-:
>>
>>  :-)  VERSION 4.6.5  (-:
>>
>>Ignoring obsolete mdp entry 'title'
>>
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.16#
>>
>> NOTE 1 [file md_SOL_rerun.mdp]:
>>nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>>nstcomm to nstcalcenergy
>>
>> Generated 168 of the 1653 non-bonded parameter combinations
>> Excluding 3 bonded neighbours molecule type 'M_R'
>> turning all bonds into constraints...
>> Excluding 2 bonded neighbours molecule type 'SOL'
>> turning all bonds into constraints...
>>
>> NOTE 2 [file topol.top]:
>>The largest charge group contains 11 atoms.
>>Since atoms only see each other when the centers of geometry of the
>> charge
>>groups they belong to are within the cut-off distance, too large charge
>>groups can lead to serious cut-off artifacts.
>>For efficiency and accuracy, charge group should consist of a few
>> atoms.
>>For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
>>
>> Analysing residue names:
>> There are: 1  Other residues
>> There are:   859  Water residues
>> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
>> into groups...
>> Number of degrees of freedom in T-Coupling group M_R is 106.94
>> Number of degrees of freedom in T-Coupling group SOL is 5151.06
>> Largest charge group radii for Van der Waals: 0.370, 0.293 nm
>> Largest charge group radii for Coulomb:   0.370, 0.307 nm
>>
>> NOTE 3 [file md_SOL_rerun.mdp]:
>>The sum of the two largest charge group radii (0.676770) is larger than
>>rlistlong (1.40) - rcoulomb (0.90).
>>With exact cut-offs, better performance can be obtained with
>>cutoff-scheme = Verlet, because it does not use charge groups at all.
>>
>> This run will generate roughly 199 Mb of data
>>
>> There were 3 notes
>>
>> Back Off! I just backed up md_sol_rerun.tpr to ./#md_sol_rerun.tpr.2#
>>
>> gcq#139: "We All Get the Flu, We All Get Aids" (LIVE)
>>
>> cbb@cbb-Precision-T1700:~/Desktop/md_ligand_RJC02836$ mdrun -s
>> md_sol_rerun.tpr -rerun md_sol.xtc
>>   :-)  G  R  O  M  A  C  S  (-:
>>
>>  Georgetown Riga Oslo