[gmx-users] GROMACS/CPMD wavefunction optimize

[limingru]

Hi everyone,I'm trying to study on the damage of base by free hydroxyl 
radicals using GROMACS-CPMD program. However, error occurred in optimization of 
wave function. Would everyone tell me wheher the interface GMX and the OPTIMIZE 
option cannot be used at the same time? if permitted, How did I do?  Please see 
the relatedcontent of the CPMD_inp.tmpl and em.mdp. Thanks in advance.
#CPMD_inp.tmpl
   INTERFACE GMX PCGFIRST
   MOLECULE CENTER OFF
   PCG MINIMIZE
   OPTIMIZE WAVEFUNCTION
   LSD



  FUNCTIONAL BLYP
  GRADIENT CORRECTION BECKE88 LYP
  LDA CORRELATION LYP
  GC-CUTOFF
  1.D-6



   POISSON SOLVER TUCKERMAN
   SYMMETRY
   0
   ANGSTROM
   CELL 
   29.555 0.6398 0.92862 0.0 0.0 0.0
   MULTIPLICITY
   2
   CUTOFF
   40.0
   CHARGE
   -0.40999



*H_VDB_PBE.psp FORMATTED
  LMAX=S
*O_VDB_PBE.psp FORMATTED
  LMAX=P
*C_VDB_PBE.psp FORMATTED
  LMAX=P
*N_VDB_PBE.psp FORMATTED
  LMAX=P

#em.mdpconstraints =  all-bonds
integrator  =  steep
constraint_algorithm= shake
QMMM=  yes
QMmethod=  CPMD
QMMMscheme  =  normal
QMMM-grps   =  QM 
QMbasis =  STO-3G
QMcharge  = -0.40999
QMmult = 2
planewavecutoff =  45
qmmmcoul_cutoff =  45
MMlayer_radii   =  10 10
MMlayer_updfqs  =  1  1
qmbox_cpmd  =  29.555 18.91 27.445



School of Nuclear Sci and Tec,
Beijing Normal University

Room.110,Teaching-Research Complex,
NO.10 WenHuiYuan St,Haiding District,
Beijing 100089,China  

E-mail: mr...@sina.com 
mr...@mail.bnu.edu.cn
Tel: +86-138-828-55737


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[gmx-users] Reg. thread MPI errror with gromacs-2016.4

[가디 장데부 고라크스나트]

Hello experts,I ran a MD simulation on HPC where Gromacs-2016.4 installed on 
GPU.I run the production simulation using job file and it terminated with the 
fatal error: setting the number of thread-MPI ranks is only supported with 
thread-MPI and Gromacs was compiled without thread-MPI. Please guide me in 
setting the gromacs-GPU related option to run simulation without an error. 
#!/bin/sh#SBATCH --job-name=test#SBATCH --partition=dual_v100_node#SBATCH 
--nodes=2#SBATCH --ntask=20#SBATCH --time=24:00:00#SBATCH 
--nodelist=tesla[21-22]#SBATCH --gres=gpu:2srun 
/applic/applications/gromacs/2016.4/bin/gmx_mpi mdrun -deffnm step7_production 
-ntmpi 4 -ntomp 10 -pin onRegards,ChangdevDr. Changdev G. GadhePost-Doc 
Researcher,Convergence Research Center for Diagnosis, Treatment and Care System 
of Dementia,Korea Institute of Science and Technology, Hwarangno 14-gil 5, 
Seongbuk-gu, Seoul 136-791, Korea Ph.: +82-10-2779-1546 , Lab: 
+82-02-958-6850Email: f07...@kist.re.kr
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[gmx-users] Reg. thread MPI errror with gromacs-2016.4

[가디 장데부 고라크스나트]

Hello experts,I ran a MD simulation on HPC where Gromacs-2016.4 installed on 
GPU.I run the production simulation using job file and it terminated with the 
fatal error: setting the number of thread-MPI ranks is only supported with 
thread-MPI and Gromacs was compiled without thread-MPI. Please guide me in 
setting the gromacs-GPU related option to run simulation without an error. 
#!/bin/sh#SBATCH --job-name=test#SBATCH --partition=dual_v100_node#SBATCH 
--nodes=2#SBATCH --ntask=20#SBATCH --time=24:00:00#SBATCH 
--nodelist=tesla[21-22]#SBATCH --gres=gpu:2srun 
/applic/applications/gromacs/2016.4/bin/gmx_mpi mdrun -deffnm step7_production 
-ntmpi 4 -ntomp 10 -pin onRegards,ChangdevDr. Changdev G. GadhePost-Doc 
Researcher,Convergence Research Center for Diagnosis, Treatment and Care System 
of Dementia,Korea Institute of Science and Technology, Hwarangno 14-gil 5, 
Seongbuk-gu, Seoul 136-791, Korea Ph.: +82-10-2779-1546 , Lab: 
+82-02-958-6850Email: f07...@kist.re.kr
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[gmx-users] Surface Tension: equation and tail corrections?

[Eric Smoll]

Hello GROMACS users,

I am using gromacs 2018.1

The manual and the gmx energy help page does not explicitly explain how the
"(surface tension) x (surface number)" is calculated.  I assume it is
equation 3.69:
L_{z} ( P_{zz}(t) - ( 0.5*P_{xx}(t) + 0.5*P_{yy}(t) ) )

Has anyone implemented a tool to compute analytical tail corrections for
the surface tension of a system with a slab structure? Assuming the there
are no excluded pairs beyond the cutoff, it seems like you can calculate
these corrections from "gmx density" number-density profiles and topology
information on the dispersive LJ term of all unique atomtypes.

Best,
Eric
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[gmx-users] question about Gromacs 5.0.4 build

[Susan Chacko]

Hi all,

I had installed Gromacs 5.0.4  on a Centos6 system a few years ago, and 
it was fine. We recently migrated our systems to Centos7, where Gromacs 
2018 was installed, also without problems.  A user requested the old 
Gromacs 5.0.4 on the Centos7 system to complete a project.


I worked through the identical install process, but of course with a 
newer compiler. The build of Gromacs went fine, but when I got to 'make 
check', one of the tests gave an error.



->  13 - SelectionUnitTests (Failed)
[ RUN  ] SelectionCollectionDataTest.HandlesCharge
/usr/local/src/gromacs/gromacs-5.0.4/src/testutils/refdata.cpp:868: Failure
Value of: strValue
  Actual: "6"
Expected: refStrValue
Which is: "5"
Google Test trace:
/usr/local/src/gromacs/gromacs-5.0.4/src/testutils/refdata.cpp:861: Checking 
'/Compiled/Selection1/Atoms/Length'
/usr/local/src/gromacs/gromacs-5.0.4/src/gromacs/selection/tests/selectioncollection.cpp:312:
 Checking selection "charge < 0.5"
/usr/local/src/gromacs/gromacs-5.0.4/src/testutils/refdata.cpp:575: Failure
Failed
Reference data item not found
Google Test trace:
/usr/local/src/gromacs/gromacs-5.0.4/src/testutils/refdata.cpp:861: Checking 
'/Compiled/Selection1/Atoms/[5]'
/usr/local/src/gromacs/gromacs-5.0.4/src/gromacs/selection/tests/selectioncollection.cpp:312:
 Checking selection "charge < 0.5"
[  FAILED  ] SelectionCollectionDataTest.HandlesCharge (1 ms)


The build completed ok, and the user reports that all their tests ran 
fine. Here are the differences between the compiles:


Centos6: Intel compiler 2015.1.133, OpenMPI 1.8.4, instruction set AVX256

Centos7: Intel compiler 2017.4.196, OpenMPI 2.1.2, instruction set SSE4.1

The cmake versions were also different, but that seems minor.

Does anyone have any thoughts about the error above? Should I try 
rebuilding with GCC? Is the Gromacs that I built safe to use :-)?


All suggestions much appreciated,

Susan

--
Susan Chacko, Ph.D.
HPC @ NIH Staff

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Re: [gmx-users] Position restrain in umbrella sampling

[rose rahmani]

I checked it for each window. it just oscillates just for 0.1nm in each
window and results are ok.
I just asked to realize your main purpose ...
And i'm convinced now ;) .
Thank you for your kindly and detailed answers like always.

Best regards
-Rose

On Wed, 6 Jun 2018, 20:01 Justin Lemkul,  wrote:

>
>
> On 6/6/18 11:18 AM, rose rahmani wrote:
> > Hi,
> >
> > I'm doing umbrella sampling for different distances of amino acid from
> > surface.
> > I know that dear Justin warns people that position restraint was for that
> > specific situation in the article mentioned in tutorial and 
> > I know it doesn't make a sense in my system too in PULLING. But i don't
> > understand why it's not usable for the rest; i mean in nvt_umbrella for
> > each window and conformation. I extract different conformations to show
> the
> > potential of mean force on that exact distance. So if i don't use
> position
> > restraint for AA in for example 0.5nm distance from surface so i can't
> > claim that this nvt_umbrella run is showing the system manner in a
> > situation that AA is about 0.5 from surface because without position
> > restraint(for AA) the AA can be anywhere in box ... . ( i should mention
> > that surface is frozen in my system)Would you please correct me if i'm
> > wrong?
>
> You shouldn't be layering biases upon biases to try to force a certain
> behavior. It is possible to combine various restraints as long as the
> resulting PMF is corrected for these effects.
>
> For each window, you define an origin of the umbrella potential. If
> that's 0.5 nm and the specified COM distance (or whatever) does not
> oscillate about this value, then there are two possibilities: (1) Your
> force constant is not large enough or (2) the physical forces in your
> system are such that it is not physically reasonable for the entities to
> exist at that interaction distance.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
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Re: [gmx-users] [EXT] Re: Water in hydrophobic core of POPC lipid bilayer

[Justin Lemkul]

On 6/6/18 11:38 AM, Smith, Iris wrote:

Hi Dallas,

Thank you so much for your expedient response. I increased the radius from 
0.375 to 0.600 however upon solvation, the water filled the hydrophobic core 
again, albeit not as much as the initial solvation (at radius 0.375 added 6338 
water molecules; at radius 0.600 added 4672 water molecules).


Contact me off-list and I will send you a script that will remove the 
waters. It is clear that simply increasing radii is no longer an 
effective approach, likely due to changes in other atomic radii that 
have been implemented recently.


I will be updating my membrane protein tutorial with a better method.

-Justin


Should I increase the radius again until it pushes all the water out? If so, by 
what increment?

Iris

  


Iris Nira Smith  |  Postdoctoral Fellow |  Genomic Medicine Institute
Cleveland Clinic  |  9500 Euclid Ave. / NE5-255  |  Cleveland, OH 44195  | 
(216) 445-7885
  
  


On 6/4/18, 12:42 AM, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of 
Dallas Warren"  wrote:

 Iris, simply increase the radius until the water is excluded. This
 parameter has no impact on the simulation, just where the water molecules
 can be placed when it is being solvated
 
 
 On Sat, 2 Jun. 2018, 7:21 am Smith, Iris,  wrote:
 
 > Hello,

 >
 > I have successfully completed the KALP-15 in DPPC membrane tutorial
 > recently and have since moved on to setting up my own protein-membrane
 > system.
 >
 > For my system I am using POPC lipid parameters with GROMOS 53a6 ff
 > obtained from the Lipidbook (2010 Poger and Mark version). After 
solvating
 > my system, water flooded the hydrophobic core within the POPC lipid
 > bilayer.  I have modified the vdw for the carbon atoms by increasing from
 > 0.15 to 0.375. However, I don’t want to arbitrarily increase the vdw 
again
 > without possibly causing artificial voids around my protein.
 >
 > Can someone offer suggestions? Thank you for your help.
 >
 > Best,
 > Iris
 >
 >
 >
 >
 >
 > ===
 >
 >
 >  Please consider the environment before printing this e-mail
 >
 > Cleveland Clinic is currently ranked as the No. 2 hospital in the country
 > by U.S. News & World Report (2017-2018). Visit us online at
 > http://www.clevelandclinic.org for a complete listing of our services,
 > staff and locations. Confidentiality Note: This message is intended for 
use
 > only by the individual or entity to which it is addressed and may contain
 > information that is privileged, confidential, and exempt from disclosure
 > under applicable law. If the reader of this message is not the intended
 > recipient or the employee or agent responsible for delivering the message
 > to the intended recipient, you are hereby notified that any 
dissemination,
 > distribution or copying of this communication is strictly prohibited. If
 > you have received this communication in error, please contact the sender
 > immediately and destroy the material in its entirety, whether electronic 
or
 > hard copy. Thank you.
 > --
 > Gromacs Users mailing list
 >
 > * Please search the archive at
 > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 > posting!
 >
 > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 >
 > * For (un)subscribe requests visit
 > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 > send a mail to gmx-users-requ...@gromacs.org.
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===


  Please consider the environment before printing this e-mail

Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. 
News & World Report (2017-2018). Visit us online at 
http://www.clevelandclinic.org for a complete listing of our services, staff and 
locations. Confidentiality Note: This message is intended for use only by the 
individual or entity to which it is addressed and may contain information that is 
privileged, confidential, and exempt from disclosure under applicable law. If the 
reader of this message is not the intended recipient or the employee or agent 
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strictly prohibited. If you have received this communication in error, please 
contact the sender 

Re: [gmx-users] [EXT] Re: Water in hydrophobic core of POPC lipid bilayer

[Smith, Iris]

Hi Dallas,

Thank you so much for your expedient response. I increased the radius from 
0.375 to 0.600 however upon solvation, the water filled the hydrophobic core 
again, albeit not as much as the initial solvation (at radius 0.375 added 6338 
water molecules; at radius 0.600 added 4672 water molecules).

Should I increase the radius again until it pushes all the water out? If so, by 
what increment?

Iris

 

Iris Nira Smith  |  Postdoctoral Fellow |  Genomic Medicine Institute
Cleveland Clinic  |  9500 Euclid Ave. / NE5-255  |  Cleveland, OH 44195  | 
(216) 445-7885
 
 

On 6/4/18, 12:42 AM, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on 
behalf of Dallas Warren"  wrote:

Iris, simply increase the radius until the water is excluded. This
parameter has no impact on the simulation, just where the water molecules
can be placed when it is being solvated


On Sat, 2 Jun. 2018, 7:21 am Smith, Iris,  wrote:

> Hello,
>
> I have successfully completed the KALP-15 in DPPC membrane tutorial
> recently and have since moved on to setting up my own protein-membrane
> system.
>
> For my system I am using POPC lipid parameters with GROMOS 53a6 ff
> obtained from the Lipidbook (2010 Poger and Mark version). After solvating
> my system, water flooded the hydrophobic core within the POPC lipid
> bilayer.  I have modified the vdw for the carbon atoms by increasing from
> 0.15 to 0.375. However, I don’t want to arbitrarily increase the vdw again
> without possibly causing artificial voids around my protein.
>
> Can someone offer suggestions? Thank you for your help.
>
> Best,
> Iris
>
>
>
>
>
> ===
>
>
>  Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the country
> by U.S. News & World Report (2017-2018). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended for 
use
> only by the individual or entity to which it is addressed and may contain
> information that is privileged, confidential, and exempt from disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the message
> to the intended recipient, you are hereby notified that any dissemination,
> distribution or copying of this communication is strictly prohibited. If
> you have received this communication in error, please contact the sender
> immediately and destroy the material in its entirety, whether electronic 
or
> hard copy. Thank you.
> --
> 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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===


 Please consider the environment before printing this e-mail

Cleveland Clinic is currently ranked as the No. 2 hospital in the country by 
U.S. News & World Report (2017-2018). Visit us online at 
http://www.clevelandclinic.org for a complete listing of our services, staff 
and locations. Confidentiality Note: This message is intended for use only by 
the individual or entity to which it is addressed and may contain information 
that is privileged, confidential, and exempt from disclosure under applicable 
law. If the reader of this message is not the intended recipient or the 
employee or agent responsible for delivering the message to the intended 
recipient, you are hereby notified that any dissemination, distribution or 
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communication in error, please contact the sender immediately and destroy the 
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mail to 

Re: [gmx-users] Position restrain in umbrella sampling

[Justin Lemkul]

On 6/6/18 11:18 AM, rose rahmani wrote:

Hi,

I'm doing umbrella sampling for different distances of amino acid from
surface.
I know that dear Justin warns people that position restraint was for that
specific situation in the article mentioned in tutorial and 
I know it doesn't make a sense in my system too in PULLING. But i don't
understand why it's not usable for the rest; i mean in nvt_umbrella for
each window and conformation. I extract different conformations to show the
potential of mean force on that exact distance. So if i don't use position
restraint for AA in for example 0.5nm distance from surface so i can't
claim that this nvt_umbrella run is showing the system manner in a
situation that AA is about 0.5 from surface because without position
restraint(for AA) the AA can be anywhere in box ... . ( i should mention
that surface is frozen in my system)Would you please correct me if i'm
wrong?


You shouldn't be layering biases upon biases to try to force a certain 
behavior. It is possible to combine various restraints as long as the 
resulting PMF is corrected for these effects.


For each window, you define an origin of the umbrella potential. If 
that's 0.5 nm and the specified COM distance (or whatever) does not 
oscillate about this value, then there are two possibilities: (1) Your 
force constant is not large enough or (2) the physical forces in your 
system are such that it is not physically reasonable for the entities to 
exist at that interaction distance.


-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Virtual sites causing npt simulation instabilities

[Justin Lemkul]

On 6/6/18 11:13 AM, Eisenhart, Andrew (eisenhaw) wrote:

new link with sole mdp file

https://files.fm/u/cmyg863c


This system doesn't even survive energy minimization for me, suggesting 
that the topology is not stable. The machine I'm on uses GROMACS 2016.3. 
Please upgrade to at least that version, if not 2018.1, because 5.1.2 is 
not even the terminal version in that series.


Your topology specifies a SETTLE geometry for an SPC-like water, which 
immediately leads to each of your waters (which have O-H distances of 
0.181 nm and H-H of 0.286 nm) to shrink inward, also shifting your 
virtual sites. That minimization simply crashes. I changed the SETTLE 
geometry to agree with your initial geometry, and while the atomic sites 
are OK, the qh1 and qh2 virtual sites expand outward, and though EM 
finishes, the max force is on the order of 10^8.


Check your virtual site construction, as this may be the source of the 
buildup in force. Use "nstxout = 1" in your em.mdp to see this happening 
more clearly.


Your cutoffs are bizarrely short but don't seem to be a problem. Once 
you've sorted out your topology issues, make sure your physical model is 
sane with such tiny cutoffs.


-Justin



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

Sent: Tuesday, June 5, 2018 9:30 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 9:28 PM, Eisenhart, Andrew (eisenhaw) wrote:

Sorry about that, he’s a another link to the same files with the fixed em.mdp. 
I hope the 7zip format is ok.

Please use tgz or just upload a plain-text em.mdp.

-Justin


https://files.fm/u/r65e3kzq

[https://files.fm/images/files.fm-fb.png]

2018-06-06_r65e3kzq
files.fm
Fast, Secure and Easy cloud file hosting, storage and safe sharing. FTP 
alternative. Free signup. Unlimited download traffic via torrents.



Andrew E. Eisenhart
Graduate Research Assistant | University of Cincinnati
330.383.5061

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

Sent: Tuesday, June 5, 2018 7:05:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote:

Here's the link to the files, if there's anything else I can send let me know. 
I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 
for the nvt and npt simulations.


em.mdp is some corrupted binary file. Please upload a corrected version.

-Justin




https://files.fm/u/c9uef9qh



Thanks

Andrew


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

Sent: Tuesday, June 5, 2018 12:54:50 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote:

Hello again,

I have done a few things since I last updated this list.


I generated a new system of only 1000 water instead of the original 2000, I 
used a more careful approach in my energy minimization, minimizing first with 
all bonds and angles constrained then again without those hash constraints. 
This succeeded in getting the maximum force in my system to below 100kcal 
without lincs warnings.


Then I proceeded to equilibrate the temperature as before with no issues, and 
finally I attempted to equilibrate the box size  using the Berendsen barostat 
running for 2ns. The box size increases as before and still does not converge. 
The system stays at around 300K, but after a while (~1ns) it seems to fill the 
box like its a gas visually at least.

So any ideas that I could try would be appreciated.

If you can assemble a tarball that contains starting coordinates (not
minimized), topology, all .mdp files, and a run script that gives the
exact sequence of what you're doing, and post it somewhere to share, I
will try to take a look at it and see if I can reproduce the behavior.

What version of GROMACS are you using?

-Justin


Thanks,

Andrew


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Eisenhart, Andrew 
(eisenhaw) 
Sent: Thursday, May 31, 2018 1:51:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hey,

Thanks for everyone's response.


I have tried using the berendsen barostat, with it I see similar behavior with 
the unit cell jumping up in size and then steadily increasing in size. I have 
some longer runs using it running now (2-3ns), so I'll be able to see it it 
eventually converges.


Nice catch with the particle type being incorrect, but with it corrected I'm 
still having the same problems (ie the oscillation of the box size) it has yet 
to 

[gmx-users] Position restrain in umbrella sampling

[rose rahmani]

Hi,

I'm doing umbrella sampling for different distances of amino acid from
surface.
I know that dear Justin warns people that position restraint was for that
specific situation in the article mentioned in tutorial and 
I know it doesn't make a sense in my system too in PULLING. But i don't
understand why it's not usable for the rest; i mean in nvt_umbrella for
each window and conformation. I extract different conformations to show the
potential of mean force on that exact distance. So if i don't use position
restraint for AA in for example 0.5nm distance from surface so i can't
claim that this nvt_umbrella run is showing the system manner in a
situation that AA is about 0.5 from surface because without position
restraint(for AA) the AA can be anywhere in box ... . ( i should mention
that surface is frozen in my system)Would you please correct me if i'm
wrong?

Best regards
-Rose
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Re: [gmx-users] Virtual sites causing npt simulation instabilities

[Eisenhart, Andrew (eisenhaw)]

new link with sole mdp file

https://files.fm/u/cmyg863c


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

Sent: Tuesday, June 5, 2018 9:30 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities



On 6/5/18 9:28 PM, Eisenhart, Andrew (eisenhaw) wrote:
> Sorry about that, he’s a another link to the same files with the fixed 
> em.mdp. I hope the 7zip format is ok.

Please use tgz or just upload a plain-text em.mdp.

-Justin

> https://files.fm/u/r65e3kzq
[https://files.fm/images/files.fm-fb.png]

2018-06-06_r65e3kzq
files.fm
Fast, Secure and Easy cloud file hosting, storage and safe sharing. FTP 
alternative. Free signup. Unlimited download traffic via torrents.


>
> Andrew E. Eisenhart
> Graduate Research Assistant | University of Cincinnati
> 330.383.5061
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Justin 
> Lemkul 
> Sent: Tuesday, June 5, 2018 7:05:51 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities
>
>
>
> On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote:
>> Here's the link to the files, if there's anything else I can send let me 
>> know. I've been using 5.1.1 for the initial set up and energy minimization, 
>> and 5.1.2 for the nvt and npt simulations.
>>
> em.mdp is some corrupted binary file. Please upload a corrected version.
>
> -Justin
>
>> 
>>
>> https://files.fm/u/c9uef9qh
>>
>>
>>
>> Thanks
>>
>> Andrew
>>
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>>  on behalf of Justin 
>> Lemkul 
>> Sent: Tuesday, June 5, 2018 12:54:50 PM
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities
>>
>>
>>
>> On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote:
>>> Hello again,
>>>
>>> I have done a few things since I last updated this list.
>>>
>>>
>>> I generated a new system of only 1000 water instead of the original 2000, I 
>>> used a more careful approach in my energy minimization, minimizing first 
>>> with all bonds and angles constrained then again without those hash 
>>> constraints. This succeeded in getting the maximum force in my system to 
>>> below 100kcal without lincs warnings.
>>>
>>>
>>> Then I proceeded to equilibrate the temperature as before with no issues, 
>>> and finally I attempted to equilibrate the box size  using the Berendsen 
>>> barostat running for 2ns. The box size increases as before and still does 
>>> not converge. The system stays at around 300K, but after a while (~1ns) it 
>>> seems to fill the box like its a gas visually at least.
>>>
>>> So any ideas that I could try would be appreciated.
>> If you can assemble a tarball that contains starting coordinates (not
>> minimized), topology, all .mdp files, and a run script that gives the
>> exact sequence of what you're doing, and post it somewhere to share, I
>> will try to take a look at it and see if I can reproduce the behavior.
>>
>> What version of GROMACS are you using?
>>
>> -Justin
>>
>>> Thanks,
>>>
>>> Andrew
>>>
>>> 
>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>>>  on behalf of Eisenhart, 
>>> Andrew (eisenhaw) 
>>> Sent: Thursday, May 31, 2018 1:51:51 PM
>>> To: gmx-us...@gromacs.org
>>> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities
>>>
>>> Hey,
>>>
>>> Thanks for everyone's response.
>>>
>>>
>>> I have tried using the berendsen barostat, with it I see similar behavior 
>>> with the unit cell jumping up in size and then steadily increasing in size. 
>>> I have some longer runs using it running now (2-3ns), so I'll be able to 
>>> see it it eventually converges.
>>>
>>>
>>> Nice catch with the particle type being incorrect, but with it corrected 
>>> I'm still having the same problems (ie the oscillation of the box size) it 
>>> has yet to throw lincs warnings though (even at ts = 2fs) so I'm going to 
>>> simulate for a longer amount of time to see if it will converge.
>>>
>>>
>>> Thanks again for everyone's reply, below is my .itp in its entirety maybe 
>>> there is an error in the exceptions(which im still not 100% sure about) or 
>>> something else that will stand out.
>>>
>>>
>>> Andrew
>>>
>>>
>>> ;
>>>
>>> [ atomtypes ]
>>> ; name  bond_typemasscharge   ptype  sigma  epsilon
>>>  qm1   qm1 0.000   -2.516V  0.000  0.000
>>>  qh1   qh1 0.0001.258V  0.000  0.000
>>>
>>> [ moleculetype ]
>>> ; molname   nrexcl
>>> M3  3
>>>
>>> [ atoms ]
>>> ; idat type res nr  residu name at name cg nr   charge
>>> 1   opls_1131   M3  OW 1   0.0
>>> 2   opls_1141   M3   

[gmx-users] What are SAsteps?

[Rafa Risnik]

Hello all,

I would like to perform a QM/MM simulation in gromacs, but when I run
grompp, it asks for the value of SAsteps. I searched online for the meaning
of this parameter and did not find anything. Can anyone please clarify what
is the meaning of SAsteps, please?

Thanks in advance and Best Regards,

Rafael
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Re: [gmx-users] g_trjorder output

[Justin Lemkul]

On 6/6/18 5:47 AM, Apramita Chand wrote:

  Dear All,
I want to choose a cutoff of 0.45nm and want to calculate the no. of urea
molecules within 0.45 as well as beyond 0.45nm of the peptide backbone(for
calculation of preferential interaction coefficient)
I have a total of 18 urea molecules in my system.
I have tried the g_trjorder command giving reference group as Backbone.

When I give the command,
g_trjorder -f 100ns_nc_72um2.xtc -s md.tpr -nshell nshell_urea.xvg -r 0.45
-da 0

I am getting reasonable no.of urea molecules like 6,8,9,etc.  Same goes for
water molecules.

But when I add -com option, all of the numbers decrease to 0 or 1. The
problem persists even on increasing the no. of urea molecules to 40 or 80.

So is it wrong to add -com option? Considering we're already specifying -da
as 0?


It is very unlikely that many molecules satisfy a COM distance cutoff of 
0.45 nm. Whereas that is a suitable cutoff for atom-atom distance, using 
the COM as the metric will require a different value.


-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 170, Issue 27

[Justin Lemkul]

On 6/6/18 2:12 AM, Muthukumaran Rajagopalan wrote:

thank you for the reply Justin.

though the APL looks close to the acceptable range, I am afraid the SN1 and SN2 
acyl chain parameters are not in the range as reported by  Pluhackova, K et al 
J. Phys. Chem. B 2016, 120, 3888?3903 and also the membrane thickness increases.


Increasing thickness and decreasing APL are physically linked, so that 
makes sense.


What "range" of values are you getting, and how much do they differ? 
What is the error bar? There's only one relevant plot in the paper you 
reference, so it's hard to tell from a simple qualitative comparison 
with no error bars.


Also note that your .mdp file posted yesterday was set to 310 K, the 
published work was 308 K. While I don't expect a big difference, note 
that you're not doing a truly apples-to-apples comparison.


Your .mdp settings are correct. The published paper makes no reference 
to the switching scheme used, other than to say that Verlet is 
equivalent to a switching function (which is far too vague for my 
liking) so you should attempt to get input files from the corresponding 
author to verify that the approaches are the same. CHARMM lipid 
parameters absolutely require a force-switch, which some people neglect 
to do properly.


-Justin

  





--

Message: 3
Date: Tue, 5 Jun 2018 19:08:45 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] mdp-settings for charmm36 and lipid apl
values
Message-ID: <8f727384-96db-e744-73b8-b1f2bbe71...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 6/5/18 1:03 PM, Muthukumaran Rajagopalan wrote:

Dear Gromacs Users,


I have recently started performing membrane simulations in gromacs 5.01 
version, I have started running simulations with pure POPE bilayer constructed 
from charmm-gui membrane builder with XY dimension 70 angs (84 lipids in each 
bilayer). The bilayer is solvated with 0.15 mol of KCL ( as Na ions have 
problem with lipid layers). The lipid layer is solvated with hydration number 
of 36 (lipid:water ratio).


I went through a series of literature and gromacs mailing list regarding 
decrease in area per lipid and tried different combinations but the area per 
lipid decreases by 3-4 angs from the experimental values (~58 for POPE).


I have referred Pluhackova, K et al J. Phys. Chem. B 2016, 120, 3888?3903

The APL value they obtained was 55.5 A^2, so your observations are
consistent. The force field apparently underestimates APL slightly.

-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==







--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Autocorrelation functions for distance vector

[David van der Spoel]

Den 2018-06-06 kl. 11:43, skrev Apramita Chand:

Dear All,
I want to calculate the time-dependent autocorrelation function for a
peptide's end-to-end distance vector . If I use g_dist , it gives me a
dist.xvg but though -lt option is there, the lifetime.xvg file is not
generated.
Is there any command to calculate the autocorrelation function? ( I am
using GROMACS version 4.6)


Regards,
Apramita

If you are just interested in the fluctuations in the scalar distance 
gmx analyze will do the job. gmx rotacf may be an option but not sure 
whether it will work. Obviously you are using  an old version and there 
may be changes in newer versions.


--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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[gmx-users] g_trjorder output

[Apramita Chand]

 Dear All,
I want to choose a cutoff of 0.45nm and want to calculate the no. of urea
molecules within 0.45 as well as beyond 0.45nm of the peptide backbone(for
calculation of preferential interaction coefficient)
I have a total of 18 urea molecules in my system.
I have tried the g_trjorder command giving reference group as Backbone.

When I give the command,
g_trjorder -f 100ns_nc_72um2.xtc -s md.tpr -nshell nshell_urea.xvg -r 0.45
-da 0

I am getting reasonable no.of urea molecules like 6,8,9,etc.  Same goes for
water molecules.

But when I add -com option, all of the numbers decrease to 0 or 1. The
problem persists even on increasing the no. of urea molecules to 40 or 80.

So is it wrong to add -com option? Considering we're already specifying -da
as 0?

Yours sincerely,
Apramita Chand
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[gmx-users] Autocorrelation functions for distance vector

[Apramita Chand]

Dear All,
I want to calculate the time-dependent autocorrelation function for a
peptide's end-to-end distance vector . If I use g_dist , it gives me a
dist.xvg but though -lt option is there, the lifetime.xvg file is not
generated.
Is there any command to calculate the autocorrelation function? ( I am
using GROMACS version 4.6)


Regards,
Apramita
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Re: [gmx-users] Fwd: H2SO4 (H2PO4-) force field

[Felipe Merino]

I've tried to generate parameters for H2PO4 for Charmm in 
https://cgenff.paramchem.org/ and the results were pretty OK (at least 
in terms of penalties).


Best

Felipe


On 06/06/18 10:22, Ondrej Kroutil wrote:

Hi gromacs user,
I have a favour to ask you.
Does anybody have working model of sulfuric acid and/or H2PO4- (exactly
these species with two OH groups)? I have tried to prepared one according
to various articles:

loukonen2010 - Enhancing effect of dimethylamine in sulfuric acid
nucleation in the presence of water – a computational study
canales2016 - A comparative molecular dynamics study of sulfuric and
methanesulfonic acids
ding2003 - Reliable potential for small sulfuric acid–water clusters
margreitter2017 - Update on phosphate and charged post‐translationally
modified amino acid parameters in the GROMOS force field -- dihedrals from
this study were used with Loukonen params.

but very often these models were unstable (or I should say my
implementations of these models were unstable) and after several
nanoseconds I got LINCS warning followed by a collapse of the oxoacid
structure and forced end of the simulation. I attach my implementation of
mentioned models and mdp file I use to run this simulations.

I bet the problem is connected to dihedrals O-P(S)-O-H but I'm not hundred
percent sure.

I'll be glad for every .itp file you can offer me.

Thank a lot and have a nice day.

 Ondřej Kroutil

https://scholar.google.cz/citations?user=vFX-JpoJ=cs

--
Ondřej Kroutil
 ,,  Faculty of Science
"))' University of South Bohemia
  OOO   Branisovska 1760, Ceske Budejovice, 370 05
   OOO  The Czech Republic
 | OO E-mail:  okrou...@gmail.com

--O Mobile:  +420 736 537 190


--
Felipe Merino,
Max Planck Institute for Molecular Physiology
Department of Structural Biochemistry
Otto-Hahn-Str. 11
44227 Dortmund
Phone: +49 231 133 2307

ORCID:  https://orcid.org/-0003-4166-8747
Publons: https://publons.com/a/1305699/
Researchgate: https://www.researchgate.net/profile/Felipe_Merino

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[gmx-users] Fwd: H2SO4 (H2PO4-) force field

[Ondrej Kroutil]

Hi gromacs user,
I have a favour to ask you.
Does anybody have working model of sulfuric acid and/or H2PO4- (exactly
these species with two OH groups)? I have tried to prepared one according
to various articles:

loukonen2010 - Enhancing effect of dimethylamine in sulfuric acid
nucleation in the presence of water – a computational study
canales2016 - A comparative molecular dynamics study of sulfuric and
methanesulfonic acids
ding2003 - Reliable potential for small sulfuric acid–water clusters
margreitter2017 - Update on phosphate and charged post‐translationally
modified amino acid parameters in the GROMOS force field -- dihedrals from
this study were used with Loukonen params.

but very often these models were unstable (or I should say my
implementations of these models were unstable) and after several
nanoseconds I got LINCS warning followed by a collapse of the oxoacid
structure and forced end of the simulation. I attach my implementation of
mentioned models and mdp file I use to run this simulations.

I bet the problem is connected to dihedrals O-P(S)-O-H but I'm not hundred
percent sure.

I'll be glad for every .itp file you can offer me.

Thank a lot and have a nice day.

Ondřej Kroutil

https://scholar.google.cz/citations?user=vFX-JpoJ=cs

--
Ondřej Kroutil
,,  Faculty of Science
   "))' University of South Bohemia
 OOO   Branisovska 1760, Ceske Budejovice, 370 05
  OOO  The Czech Republic
| OO E-mail:  okrou...@gmail.com
>--O Mobile:  +420 736 537 190
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 170, Issue 27

[Muthukumaran Rajagopalan]

thank you for the reply Justin.

though the APL looks close to the acceptable range, I am afraid the SN1 and SN2 
acyl chain parameters are not in the range as reported by  Pluhackova, K et al 
J. Phys. Chem. B 2016, 120, 3888?3903 and also the membrane thickness 
increases.  
 

> 
> 
> 
> 
> --
> 
> Message: 3
> Date: Tue, 5 Jun 2018 19:08:45 -0400
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] mdp-settings for charmm36 and lipid apl
>   values
> Message-ID: <8f727384-96db-e744-73b8-b1f2bbe71...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
> 
> 
> 
> On 6/5/18 1:03 PM, Muthukumaran Rajagopalan wrote:
> > Dear Gromacs Users,
> >
> >
> > I have recently started performing membrane simulations in gromacs 5.01 
> > version, I have started running simulations with pure POPE bilayer 
> > constructed from charmm-gui membrane builder with XY dimension 70 angs (84 
> > lipids in each bilayer). The bilayer is solvated with 0.15 mol of KCL ( as 
> > Na ions have problem with lipid layers). The lipid layer is solvated with 
> > hydration number of 36 (lipid:water ratio).
> >
> >
> > I went through a series of literature and gromacs mailing list regarding 
> > decrease in area per lipid and tried different combinations but the area 
> > per lipid decreases by 3-4 angs from the experimental values (~58 for POPE).
> >
> >
> > I have referred Pluhackova, K et al J. Phys. Chem. B 2016, 120, 3888?3903
> 
> The APL value they obtained was 55.5 A^2, so your observations are 
> consistent. The force field apparently underestimates APL slightly.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> 
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
> 
> ==
> 
> 
> 
> 
> 
-- 
with regards 

R. Muthukumaran
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Re: [gmx-users] Charge groups in poly methyl methacrylic acid

[David van der Spoel]

Den 2018-06-06 kl. 05:01, skrev Debadutta Prusty:

Hi everyone,

I am new to gromacs and hence, this question might be naive. How does one
go about assigning charge groups while creating new monomer topologies in
.rtp files? What I gather from looking at similar posts is that the net
charge of a charge group should be an integer (zero for a neutral group and
positive/negative for charged groups). However, this rule does not seem to
be that straight-forward in many cases. For a polymer PMAA  (
https://en.wikipedia.org/wiki/Poly(methacrylic_acid)), the charged groups
can be CO2H, CH3,CH2. According to opls fields, these groups have a net
zero charge. However, the remaining carbon atom, which does not have a
hydrogen, has a net charge of -0.02 if I use  opls_139 (C in alkane). Is
there a way around this problem ?

Thanks,
Debadutta Prusty

This is not important anymore as long as you use PME and the appropriate 
shifting function. But your system does need to be neutral overall.


--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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