[gmx-users] Regarding viewing Trajectories

[Dilip H N]

Hello.,
In RDF of amino acid with ammonia and water mixture, i have got a 1st peak,
2nd peak (solvation shell), and i need to view this in the vmd by making
use of the trajectories (trr/xtc files), so while viewing the trajectories

1] how can i view that exact trajectory at which i have got the particular
peak in RDF (since that would mean either H-bond formation/probability of
tht molecule close to that)
because viewing each frame to find it would take literally lot of time, ...

Thank you.

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



   Sent with Mailtrack

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[gmx-users] Difference between LJ-14 and LJ(SR)

[Heng Ma]

Hi, all, 
I recently came across the calculation of intramolecular energy using g_energy 
in gromacs.There were 2 outputs, LJ-14 and LJ(SR) that I found very ambiguous 
in the explanation on the manual.I want to share my understanding with the 
community to make sure I have the right result. 1) To my knowledge, LJ-14 is 
the intramolecular interaction Only between every i and i+3 atoms.  Atom pairs  
  for LJ-14 are listed in the item of "Pair" of *top file.  2) With the default 
nrexcl = 3 is used in *top file,  LJ(SR) include intramolecular LJ energy 
between i and other atoms are more than 3 bonds away, and all intermolecular LJ 
interactions.  The interactions between i and i+1 or i+2 or i+3 inside a 
molecule were excluded from LJ(SR) term, for the default nrexcl = 3. And it is 
the same with Coul-14 and Coul(SR). Pls help me confirm whether my 
understanding is correct. Let me know if there is anything wrong with my 
understanding of those terms. 
Thanks a lot. 
Heng Mahma@lamar.eduPhD candidate,Department of Chemical Enginnering,Lamar 
University, TX. 
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[gmx-users] How to measure distance between two COM (centre of mass) of two group of atom

[Md. Imrul Reza Shishir]

Dear all
How do I measure distance between two COM (centre of mass) of two group of
atom. I want to measure the strain of my simulation system.
​[image: Inline image 3]​
​For that purpose i want to apply following ​analysis to the initial
structure and final structure to measure the distance.
​
"gmx distance -s *.tpr -f *.gro -n index.ndx -oall *.xvg​"

​Is this process is correct? What else should be the right procedure. I am
little bit confused with the output xvg file result. From where how can I
measure the distance.​

-- 
*Md Imrul Reza Shishir*
Master Student
*Inha University*
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Re: [gmx-users] Alchemical free energy

[Hannes Loeffler]

On Tue, 4 Apr 2017 18:57:50 +0200
Alex  wrote:

> In relative binding free energy calculation via alchemical free
> energy, I noticed that either the word "Decouple" or "Annihilate" is
> used. What is the difference between them?

Actually, this is typically used in the context of absolute free
energies. The meaning depends on the author, see e.g.
http://www.alchemistry.org/wiki/Decoupling_and_annihilation


> When should we use which?

See above.  In any case, make sure that you explain what your intended
meaning is.
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[gmx-users] Alchemical free energy

[Alex]

Dear gromacs user,

In relative binding free energy calculation via alchemical free energy, I
noticed that either the word "Decouple" or "Annihilate" is used. What is
the difference between them? When should we use which?

Thanks,

Alex
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Re: [gmx-users] Force Fields Keeping sp3 Nitrogen Groups Planar?

[Phillip Rauscher]

It occurs to me that an example would be helpful.  Here is an excerpt from
the OPLS aminoacids.rtp file detailing alanine:


























*[ ALA ] [ atoms ]  Nopls_238   -0.500 1 Hopls_241
0.300 1 CAopls_224B   0.140 1 HAopls_140
0.060 1 CBopls_135   -0.180 2HB1opls_140
0.060 2HB2opls_1400.060 2HB3opls_140
0.060 2  Copls_2350.500 3 Oopls_236
-0.500 3 [ bonds ] N H NCACAHACACB
CA CCB   HB1CB   HB2CB   HB3 C O-C N [
impropers ]-CCA N Himproper_Z_N_X_Y CA+N
C Oimproper_O_C_X_Y *

We can see that the Nitrogen is bound to atoms H, CA, and -C (on the
previous residue).  In the [impropers] section, an improper dihedral is
defined for these four atoms (with the nitrogen in both of the dihedral
planes).  If we look at the definition of that improper in the OPLS
ffbonded.itp file, we see the following:













*[ dihedraltypes ]; Improper OPLS dihedrals to keep groups planar.; (OPLS
doesnt use impropers for chiral atoms).; Since these functions are periodic
of the form 1-cos(2*x), they are actually; implemented as proper dihedrals
[1+cos(2*x+180)] for the moment, ; to keep things compatible.; The defines
are used in ffoplsaa.rtp or directly in your .top file; Z -N?-X -Y
improper torsion#define improper_Z_N_X_Y180.0  4.18400   2*
Given the functional form and the parameters used, this potential has
minima at 0 and 180 degrees, thus keeping all four atoms (centered at the
nitrogen) in the same plane.

On Tue, Apr 4, 2017 at 10:38 AM, Phillip Rauscher 
wrote:

> Hello all,
>
> I've noticed that in some of the force fields (in the aminoacid.rtp
> files), an improper dihedral is applied to the nitrogens in the peptide
> bond (and sometimes other amine groups as well), which are all sp3
> hybridized with one lone pair.  Interestingly, the dihedral potential
> parameters serve to keep the groups trigonal planar, rather than
> tetrahedral.  More specifically, I've seen this in OPLS, Amber03, and
> Charmm27 - enough to indicate that it's not a mistake (besides the fact
> that it's applied to ALL amino acids!)  The functional form of the improper
> potential varies between force fields, but the lowest energy angle is
> always 0 or 180 indicating planar structure.
>
> Why is this done?  I've done some digging through the GROMACS publications
> as well as those for the force fields and can't seem to find any reference
> to this practice?  Is it an attempt to "average out" nitrogen inversions?
> Is it just to eliminate a chiral center?
>
> Thanks for your help!
>
> -Phil Rauscher
>
> --
> Phil Rauscher
> Graduate Student
> de Pablo and Rowan Research Groups
> Institute for Molecular Engineering
> University of Chicago
>



-- 
Phil Rauscher
Graduate Student
de Pablo and Rowan Research Groups
Institute for Molecular Engineering
University of Chicago
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[gmx-users] Force Fields Keeping sp3 Nitrogen Groups Planar?

[Phillip Rauscher]

Hello all,

I've noticed that in some of the force fields (in the aminoacid.rtp files),
an improper dihedral is applied to the nitrogens in the peptide bond (and
sometimes other amine groups as well), which are all sp3 hybridized with
one lone pair.  Interestingly, the dihedral potential parameters serve to
keep the groups trigonal planar, rather than tetrahedral.  More
specifically, I've seen this in OPLS, Amber03, and Charmm27 - enough to
indicate that it's not a mistake (besides the fact that it's applied to ALL
amino acids!)  The functional form of the improper potential varies between
force fields, but the lowest energy angle is always 0 or 180 indicating
planar structure.

Why is this done?  I've done some digging through the GROMACS publications
as well as those for the force fields and can't seem to find any reference
to this practice?  Is it an attempt to "average out" nitrogen inversions?
Is it just to eliminate a chiral center?

Thanks for your help!

-Phil Rauscher

-- 
Phil Rauscher
Graduate Student
de Pablo and Rowan Research Groups
Institute for Molecular Engineering
University of Chicago
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Re: [gmx-users] System almost blowing up

[Justin Lemkul]

On 4/4/17 9:45 AM, Dayhoff, Guy wrote:



On 4/4/17 9:31 AM, Dayhoff, Guy wrote:


On 4/3/17 2:33 PM, Dayhoff, Guy wrote:



Hi,

I?m receiving a couple (~15) EM did not converge warnings as well as a few (~3) 
1,4 interaction
warnings during my run. It looks like it starts down the path to blowing up but 
recovers. Is this ?recovery?
system dependent? Should I take these messages (even without the subsequent 
crash) to indicate an
underlying issue with my system/topology or equilibration? I?m not ignoring or 
circumventing any warning
during pdb2gmx, or any other commands.

For more context: I?m running the Drude-2013 forcefield, with a dt of .5fs 
emtol of 1.0 and niter of 150
using the V-rescale thermostat and Berendsen pressure coupling while my systems 
cell shape relaxes
as a continuation from position restrained NVT then NPT ensembles. The starting 
structures were minimized
in vacuum, then solvated and minimized once again prior to the posres 
equilibration.



Such a short dt and strict niter should not be necessary in practice.  The
failure of SCF to converge/LINCS warnings is what we typically refer to as
polarization catastrophe, so your system is on the brink of instability.  This
is one of the inherent problems of SCF in polarizable systems; it often fails to
converge and leaves the system potentially unstable.  The reflective hardwall is
much more reliable (and faster).  If the instability is happening in your
equilibration, that may be OK but it is something you should try to troubleshoot
to make sure there's nothing else going wrong.

-Justin

--



Got it. I have been spending some time investigating the issue i?m having and
after reading shellfc.cpp I was pretty confident the issue was with SCF not 
converging,
and so my niter and dt were an attempt at looking into that.

The workflow i?ve been trying to use is?
EM -> Solvate -> EM -> posres NVT V-rescale -> posres berendsen NPT isotropic 1bar 
w/ V-rescale tcoupl ->
berendsen NPT semi-isotropic various pressures w/ V-rescale tcoupl

then once my cell shape has reached an equilibrium I finally switch to NH 
thermostat and PR barostat for
the production run.

If I switch to employing the hardwall (and the lagrangian dynamics for drudes) 
then I understand it is not
compatible yet with NPT ensembles. So, if I change my work flow as follows 
would it be appropriate still?

EM->Solvate->EM->posre NPT isotropic 1 bar w/ V-rescale tcoupl->NPT 
semi-isotropic varying pressures
w V-rescale tcoupl until cell shape is equilibrated using PR barostat, then 
switch to NVT without pcoupl
to use the hardwall during my production run?

For some reason, i?ve got this idea that I need to be tcoupling and pcoupling 
during my production runs
so i?ve been apprehensive to do this.



If you want an NPT ensemble during dynamics you're going to have to use NAMD,
CHARMM, or OpenMM.  I haven't coded the barostat yet (fixing the DD bugs has
been more important).  You can equilibrate with SCF under NPT and get a suitable
density, then switch to NVT, but your use of semi-isotropic coupling suggests a
membrane system?  In that case, I would not use NVT during production as you
will be simulating a constant area, which may not be appropriate.



I?ve parameterized beta-cellulose and then an additional modified form of 
beta-cellulose for the FF
and i?m looking at the packing behavior of a bundle of strands under the 
different pressures in water.
Everything seems to be proper apart from encountering the polarization 
catastrophe randomly,
often times I can restart a downed run and it will move beyond the previous 
crash point, but this
is tedious and even when I wrote a script to do it for me I found that 
eventually there was a point
of no return, even if I used the prev_cpt.



If you have this many crashes, your physical model is not suitable.  You need to
revisit the parametrization before even thinking about more simulations.  An
occasional convergence failure with SCF during equilibration is not worrisome,
continual problems indicate a bad model.  Your tiny time step and large niter
value were clues that this is the case.

-Justin



Okay thanks. To be clear I did use a dt of 1fs and 1.25fs with niter = 50 in my 
initial runs which all
went through EM, posres NVT and NPT with scf just fine and then began to have 
issues after removing
the posres. Now that i’m writing this I suppose that is also an indication that 
the issue lies in my parameters
and the behavior of the strand once it’s allowed to move freely?



Yes, precisely.  If your run only continues if it's restrained or forced through 
by repeated restarts, it's a bad simulation.


For what it's worth, carbohydrate linkages are very complex and we're still 
working on getting all aspects of this right.  It's no surprise you're facing 
issues.  We've been working on disaccharides of all types for months :)


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth 

Re: [gmx-users] System almost blowing up

[Dayhoff, Guy]

> 
> 
> On 4/4/17 9:31 AM, Dayhoff, Guy wrote:
>>> 
>>> On 4/3/17 2:33 PM, Dayhoff, Guy wrote:
 
>> Hi,
>> 
>> I?m receiving a couple (~15) EM did not converge warnings as well as a 
>> few (~3) 1,4 interaction
>> warnings during my run. It looks like it starts down the path to blowing 
>> up but recovers. Is this ?recovery?
>> system dependent? Should I take these messages (even without the 
>> subsequent crash) to indicate an
>> underlying issue with my system/topology or equilibration? I?m not 
>> ignoring or circumventing any warning
>> during pdb2gmx, or any other commands.
>> 
>> For more context: I?m running the Drude-2013 forcefield, with a dt of 
>> .5fs emtol of 1.0 and niter of 150
>> using the V-rescale thermostat and Berendsen pressure coupling while my 
>> systems cell shape relaxes
>> as a continuation from position restrained NVT then NPT ensembles. The 
>> starting structures were minimized
>> in vacuum, then solvated and minimized once again prior to the posres 
>> equilibration.
>> 
> 
> Such a short dt and strict niter should not be necessary in practice.  The
> failure of SCF to converge/LINCS warnings is what we typically refer to as
> polarization catastrophe, so your system is on the brink of instability.  
> This
> is one of the inherent problems of SCF in polarizable systems; it often 
> fails to
> converge and leaves the system potentially unstable.  The reflective 
> hardwall is
> much more reliable (and faster).  If the instability is happening in your
> equilibration, that may be OK but it is something you should try to 
> troubleshoot
> to make sure there's nothing else going wrong.
> 
> -Justin
> 
> --
> 
 
 Got it. I have been spending some time investigating the issue i?m having 
 and
 after reading shellfc.cpp I was pretty confident the issue was with SCF 
 not converging,
 and so my niter and dt were an attempt at looking into that.
 
 The workflow i?ve been trying to use is?
 EM -> Solvate -> EM -> posres NVT V-rescale -> posres berendsen NPT 
 isotropic 1bar w/ V-rescale tcoupl ->
 berendsen NPT semi-isotropic various pressures w/ V-rescale tcoupl
 
 then once my cell shape has reached an equilibrium I finally switch to NH 
 thermostat and PR barostat for
 the production run.
 
 If I switch to employing the hardwall (and the lagrangian dynamics for 
 drudes) then I understand it is not
 compatible yet with NPT ensembles. So, if I change my work flow as follows 
 would it be appropriate still?
 
 EM->Solvate->EM->posre NPT isotropic 1 bar w/ V-rescale tcoupl->NPT 
 semi-isotropic varying pressures
 w V-rescale tcoupl until cell shape is equilibrated using PR barostat, 
 then switch to NVT without pcoupl
 to use the hardwall during my production run?
 
 For some reason, i?ve got this idea that I need to be tcoupling and 
 pcoupling during my production runs
 so i?ve been apprehensive to do this.
 
>>> 
>>> If you want an NPT ensemble during dynamics you're going to have to use 
>>> NAMD,
>>> CHARMM, or OpenMM.  I haven't coded the barostat yet (fixing the DD bugs has
>>> been more important).  You can equilibrate with SCF under NPT and get a 
>>> suitable
>>> density, then switch to NVT, but your use of semi-isotropic coupling 
>>> suggests a
>>> membrane system?  In that case, I would not use NVT during production as you
>>> will be simulating a constant area, which may not be appropriate.
>>> 
>> 
>> I?ve parameterized beta-cellulose and then an additional modified form of 
>> beta-cellulose for the FF
>> and i?m looking at the packing behavior of a bundle of strands under the 
>> different pressures in water.
>> Everything seems to be proper apart from encountering the polarization 
>> catastrophe randomly,
>> often times I can restart a downed run and it will move beyond the previous 
>> crash point, but this
>> is tedious and even when I wrote a script to do it for me I found that 
>> eventually there was a point
>> of no return, even if I used the prev_cpt.
>> 
> 
> If you have this many crashes, your physical model is not suitable.  You need 
> to 
> revisit the parametrization before even thinking about more simulations.  An 
> occasional convergence failure with SCF during equilibration is not 
> worrisome, 
> continual problems indicate a bad model.  Your tiny time step and large niter 
> value were clues that this is the case.
> 
> -Justin
> 

Okay thanks. To be clear I did use a dt of 1fs and 1.25fs with niter = 50 in my 
initial runs which all
went through EM, posres NVT and NPT with scf just fine and then began to have 
issues after removing 
the posres. Now that i’m writing this I suppose that is also an indication that 
the issue lies in my parameters
and the behavior of the 

Re: [gmx-users] CHARMM27 hates my DMPC

[Justin Lemkul]

On 4/4/17 9:39 AM, Vytautas Rakeviius wrote:

Thanks, I reused DMPC layers from CHARMM-GUI after some editing.
I was able to pin-down issue here, test file:
http://www.mediafire.com/file/usuv55c3j505ec2/test.pdb
I can do: 
gmx pdb2gmx -f test.pdb -o test.gro -water spce

Without error. But if I do: 

gmx pdb2gmx -f test.pdb -o test.gro -water spce -ignh
I get error about hydrogen which I try to ignore. Very strange for me. -ignh
option is not possible with CHARMM ff?




Sure it is, but only when applied properly.

-ignh tells pdb2gmx to ignore H atoms and try to rebuild them.  If you haven't 
constructed a suitable .hdb entry for your residue, you're just going to cause 
errors for yourself because now you've ignored atoms, which are considered missing.


-Justin




On Tuesday, April 4, 2017 3:59 PM, Justin Lemkul  wrote:




On 4/4/17 8:52 AM, Vytautas Rakeviius wrote:

Hello,
I have my system with DMPC bilayers in pdb and try to convert it into GROMACS

input. Because system is with lipids I think chose CHARMM27 ff. But still I get
lots of warnings like that:


https://pastebin.com/K8dHKkUi
Also I add my DMPC pdb as example. What should I do? Rename all my DMPC

atoms?Thanks for all suggestions.






This is the same with any force field; the atom names have to match the force
field's expectations.

If you're just trying to build a DMPC bilayer, construct one using CHARMM-GUI.
It's guaranteed to have CHARMM-compliant nomenclature (and you should be using
CHARMM36 for lipids, anyway, because the CHARMM27 parameters are not nearly as
good for lipids).

-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


==




--
==

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] CHARMM27 hates my DMPC

[Vytautas Rakeviius]

Thanks, I reused DMPC layers from CHARMM-GUI after some editing.I was able to 
pin-down issue here, test 
file:http://www.mediafire.com/file/usuv55c3j505ec2/test.pdbI can do:gmx pdb2gmx 
-f test.pdb -o test.gro -water spce
Without error. But if I do:gmx pdb2gmx -f test.pdb -o test.gro -water spce 
-ignhI get error about hydrogen which I try to ignore. Very strange for me. 
-ignh option is not possible with CHARMM ff?


 

On Tuesday, April 4, 2017 3:59 PM, Justin Lemkul  wrote:
 

 

On 4/4/17 8:52 AM, Vytautas Rakeviius wrote:
> Hello,
> I have my system with DMPC bilayers in pdb and try to convert it into GROMACS 
> input. Because system is with lipids I think chose CHARMM27 ff. But still I 
> get lots of warnings like that:
>
> https://pastebin.com/K8dHKkUi
> Also I add my DMPC pdb as example. What should I do? Rename all my DMPC 
> atoms?Thanks for all suggestions.
>
>

This is the same with any force field; the atom names have to match the force 
field's expectations.

If you're just trying to build a DMPC bilayer, construct one using CHARMM-GUI. 
It's guaranteed to have CHARMM-compliant nomenclature (and you should be using 
CHARMM36 for lipids, anyway, because the CHARMM27 parameters are not nearly as 
good for lipids).

-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] System almost blowing up

[Justin Lemkul]

On 4/4/17 9:31 AM, Dayhoff, Guy wrote:


On 4/3/17 2:33 PM, Dayhoff, Guy wrote:



Hi,

 I?m receiving a couple (~15) EM did not converge warnings as well as a few 
(~3) 1,4 interaction
warnings during my run. It looks like it starts down the path to blowing up but 
recovers. Is this ?recovery?
system dependent? Should I take these messages (even without the subsequent 
crash) to indicate an
underlying issue with my system/topology or equilibration? I?m not ignoring or 
circumventing any warning
during pdb2gmx, or any other commands.

For more context: I?m running the Drude-2013 forcefield, with a dt of .5fs 
emtol of 1.0 and niter of 150
using the V-rescale thermostat and Berendsen pressure coupling while my systems 
cell shape relaxes
as a continuation from position restrained NVT then NPT ensembles. The starting 
structures were minimized
in vacuum, then solvated and minimized once again prior to the posres 
equilibration.



Such a short dt and strict niter should not be necessary in practice.  The
failure of SCF to converge/LINCS warnings is what we typically refer to as
polarization catastrophe, so your system is on the brink of instability.  This
is one of the inherent problems of SCF in polarizable systems; it often fails to
converge and leaves the system potentially unstable.  The reflective hardwall is
much more reliable (and faster).  If the instability is happening in your
equilibration, that may be OK but it is something you should try to troubleshoot
to make sure there's nothing else going wrong.

-Justin

--



Got it. I have been spending some time investigating the issue i?m having and
after reading shellfc.cpp I was pretty confident the issue was with SCF not 
converging,
and so my niter and dt were an attempt at looking into that.

The workflow i?ve been trying to use is?
EM -> Solvate -> EM -> posres NVT V-rescale -> posres berendsen NPT isotropic 1bar 
w/ V-rescale tcoupl ->
berendsen NPT semi-isotropic various pressures w/ V-rescale tcoupl

then once my cell shape has reached an equilibrium I finally switch to NH 
thermostat and PR barostat for
the production run.

If I switch to employing the hardwall (and the lagrangian dynamics for drudes) 
then I understand it is not
compatible yet with NPT ensembles. So, if I change my work flow as follows 
would it be appropriate still?

EM->Solvate->EM->posre NPT isotropic 1 bar w/ V-rescale tcoupl->NPT 
semi-isotropic varying pressures
w V-rescale tcoupl until cell shape is equilibrated using PR barostat, then 
switch to NVT without pcoupl
to use the hardwall during my production run?

For some reason, i?ve got this idea that I need to be tcoupling and pcoupling 
during my production runs
so i?ve been apprehensive to do this.



If you want an NPT ensemble during dynamics you're going to have to use NAMD,
CHARMM, or OpenMM.  I haven't coded the barostat yet (fixing the DD bugs has
been more important).  You can equilibrate with SCF under NPT and get a suitable
density, then switch to NVT, but your use of semi-isotropic coupling suggests a
membrane system?  In that case, I would not use NVT during production as you
will be simulating a constant area, which may not be appropriate.



I’ve parameterized beta-cellulose and then an additional modified form of 
beta-cellulose for the FF
and i’m looking at the packing behavior of a bundle of strands under the 
different pressures in water.
Everything seems to be proper apart from encountering the polarization 
catastrophe randomly,
often times I can restart a downed run and it will move beyond the previous 
crash point, but this
is tedious and even when I wrote a script to do it for me I found that 
eventually there was a point
of no return, even if I used the prev_cpt.



If you have this many crashes, your physical model is not suitable.  You need to 
revisit the parametrization before even thinking about more simulations.  An 
occasional convergence failure with SCF during equilibration is not worrisome, 
continual problems indicate a bad model.  Your tiny time step and large niter 
value were clues that this is the case.


-Justin


I was able to run a single 20mer strand for 2ns without a crash, but my actual 
system has
many strands in it. Does scalability come into play here, my system is near 60k 
atoms? I
 know these features are not supported officially yet, are there any 
suggestions pertaining
 to a possible source of error to check that I wouldn’t have come across in the 
documentation or
  other forums?

I’ve been wrestling with getting the production runs going for a few weeks, 
perhaps its time to just move
to another simulation suite as you mentioned which has full implementation of 
the drude oscillators.

- Guy





--
==

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.

Re: [gmx-users] System almost blowing up

[Dayhoff, Guy]

> 
> On 4/3/17 2:33 PM, Dayhoff, Guy wrote:
>> 
 Hi,
 
  I?m receiving a couple (~15) EM did not converge warnings as well as a 
 few (~3) 1,4 interaction
 warnings during my run. It looks like it starts down the path to blowing 
 up but recovers. Is this ?recovery?
 system dependent? Should I take these messages (even without the 
 subsequent crash) to indicate an
 underlying issue with my system/topology or equilibration? I?m not 
 ignoring or circumventing any warning
 during pdb2gmx, or any other commands.
 
 For more context: I?m running the Drude-2013 forcefield, with a dt of .5fs 
 emtol of 1.0 and niter of 150
 using the V-rescale thermostat and Berendsen pressure coupling while my 
 systems cell shape relaxes
 as a continuation from position restrained NVT then NPT ensembles. The 
 starting structures were minimized
 in vacuum, then solvated and minimized once again prior to the posres 
 equilibration.
 
>>> 
>>> Such a short dt and strict niter should not be necessary in practice.  The
>>> failure of SCF to converge/LINCS warnings is what we typically refer to as
>>> polarization catastrophe, so your system is on the brink of instability.  
>>> This
>>> is one of the inherent problems of SCF in polarizable systems; it often 
>>> fails to
>>> converge and leaves the system potentially unstable.  The reflective 
>>> hardwall is
>>> much more reliable (and faster).  If the instability is happening in your
>>> equilibration, that may be OK but it is something you should try to 
>>> troubleshoot
>>> to make sure there's nothing else going wrong.
>>> 
>>> -Justin
>>> 
>>> --
>>> 
>> 
>> Got it. I have been spending some time investigating the issue i?m having and
>> after reading shellfc.cpp I was pretty confident the issue was with SCF not 
>> converging,
>> and so my niter and dt were an attempt at looking into that.
>> 
>> The workflow i?ve been trying to use is?
>> EM -> Solvate -> EM -> posres NVT V-rescale -> posres berendsen NPT 
>> isotropic 1bar w/ V-rescale tcoupl ->
>> berendsen NPT semi-isotropic various pressures w/ V-rescale tcoupl
>> 
>> then once my cell shape has reached an equilibrium I finally switch to NH 
>> thermostat and PR barostat for
>> the production run.
>> 
>> If I switch to employing the hardwall (and the lagrangian dynamics for 
>> drudes) then I understand it is not
>> compatible yet with NPT ensembles. So, if I change my work flow as follows 
>> would it be appropriate still?
>> 
>> EM->Solvate->EM->posre NPT isotropic 1 bar w/ V-rescale tcoupl->NPT 
>> semi-isotropic varying pressures
>> w V-rescale tcoupl until cell shape is equilibrated using PR barostat, then 
>> switch to NVT without pcoupl
>> to use the hardwall during my production run?
>> 
>> For some reason, i?ve got this idea that I need to be tcoupling and 
>> pcoupling during my production runs
>> so i?ve been apprehensive to do this.
>> 
> 
> If you want an NPT ensemble during dynamics you're going to have to use NAMD, 
> CHARMM, or OpenMM.  I haven't coded the barostat yet (fixing the DD bugs has 
> been more important).  You can equilibrate with SCF under NPT and get a 
> suitable 
> density, then switch to NVT, but your use of semi-isotropic coupling suggests 
> a 
> membrane system?  In that case, I would not use NVT during production as you 
> will be simulating a constant area, which may not be appropriate.
> 

I’ve parameterized beta-cellulose and then an additional modified form of 
beta-cellulose for the FF
and i’m looking at the packing behavior of a bundle of strands under the 
different pressures in water.
Everything seems to be proper apart from encountering the polarization 
catastrophe randomly,
often times I can restart a downed run and it will move beyond the previous 
crash point, but this
is tedious and even when I wrote a script to do it for me I found that 
eventually there was a point
of no return, even if I used the prev_cpt.

I was able to run a single 20mer strand for 2ns without a crash, but my actual 
system has
many strands in it. Does scalability come into play here, my system is near 60k 
atoms? I
 know these features are not supported officially yet, are there any 
suggestions pertaining
 to a possible source of error to check that I wouldn’t have come across in the 
documentation or
  other forums? 

I’ve been wrestling with getting the production runs going for a few weeks, 
perhaps its time to just move
to another simulation suite as you mentioned which has full implementation of 
the drude oscillators.

- Guy



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Re: [gmx-users] CHARMM27 hates my DMPC

[Justin Lemkul]

On 4/4/17 8:52 AM, Vytautas Rakeviius wrote:

Hello,
I have my system with DMPC bilayers in pdb and try to convert it into GROMACS 
input. Because system is with lipids I think chose CHARMM27 ff. But still I get 
lots of warnings like that:

https://pastebin.com/K8dHKkUi
Also I add my DMPC pdb as example. What should I do? Rename all my DMPC 
atoms?Thanks for all suggestions.




This is the same with any force field; the atom names have to match the force 
field's expectations.


If you're just trying to build a DMPC bilayer, construct one using CHARMM-GUI. 
It's guaranteed to have CHARMM-compliant nomenclature (and you should be using 
CHARMM36 for lipids, anyway, because the CHARMM27 parameters are not nearly as 
good for lipids).


-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] .mdp file for Enthalpy of Vaporization calculation

[Justin Lemkul]

On 4/4/17 6:21 AM, Matteo Busato wrote:

Goodmorning to everyone,


I'm writing here because I'm trying to perform a calculation about the Enthalpy 
of Vaporization of a system with 434 molecules of an ionic liquid. I've already 
read all the previous posts in the forum about this subject and it has come 
clear to me how to perform the calculation, however I'm having problems with my 
.mdp file when trying to perform the NVT equilibration.

I've read that for such calculation cutoffs must be set = 0 and pbc=none, 
however with such parameters I'm forced to use cutoff-scheme=group instead of 
Verlet, so the first problem is that 'group' is not configured for GPU 
acceleration and I can use just 1 MPI rank (which slows the job time a lot). Is 
there a way to perform this calculation with Verlet?

The second problem is that if I set rvdw=0, gromacs gives me an error saying that 
(obviously), vdw-switch must be < rvdw. How can I solve this issue?



There's nothing to switch; you're using a plain cutoff.

There's no point trying to use a GPU to simulate one molecule.  This simulation 
should run in a matter of seconds on a single CPU.


-Justin


I'll post the mdp I'm using here. Thank you in advance.


; Run control
integrator   = sd   ; Langevin dynamics
tinit= 0
dt   = 0.001
nsteps   = 100; 1000 ps
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= group
nstlist  = 0
ns_type  = grid
pbc  = no
rlist= 0
; Electrostatics
coulombtype  = cutoff
rcoulomb = 0
; van der Waals
vdwtype  = cutoff
vdw-modifier = potential-switch
rvdw = 0
rvdw-switch  =0
; 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= 298.15
; Pressure coupling is off for NVT
Pcoupl   = No
tau_p= 0.5
compressibility  = 4.5e-05
ref_p= 1.0
; Generate velocities to start
gen_vel  = yes
gen_temp = 300
gen_seed = -1
; options for bonds
constraints  = h-bonds  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Do not constrain the starting configuration
continuation = no
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 12
dispcorr=no


Matteo Busato



--
==

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] gmx insert_molecules problem

[Justin Lemkul]

On 4/4/17 2:42 AM, 吴萌 wrote:

Hi All,

  I am running a membrane protein MD simulation with Gromacs 5.1.4. I want to 
add some substrate molecules(acetate) to my system, and I used this command:
  "gmx insert_molecules -f ###.pdb(include the ptotein, POPC, etc.) -ci act.pdb -o 
###.pdb -nmol 48 -box 6.7 6.7 8.1 -try 500 -rot xyz",
  but then I found many acetate molecules are put out of the system in the out 
.pdb.
  Is that normol or wouldl affect the later MD process? If so, how can I fix it.
  Any suggestions would be greatly appreciated. Thank you in advance!



There's no such thing as "outside" of a periodic box.

-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] System almost blowing up

[Justin Lemkul]

On 4/3/17 2:33 PM, Dayhoff, Guy wrote:



Hi,

  I?m receiving a couple (~15) EM did not converge warnings as well as a few 
(~3) 1,4 interaction
warnings during my run. It looks like it starts down the path to blowing up but 
recovers. Is this ?recovery?
system dependent? Should I take these messages (even without the subsequent 
crash) to indicate an
underlying issue with my system/topology or equilibration? I?m not ignoring or 
circumventing any warning
during pdb2gmx, or any other commands.

For more context: I?m running the Drude-2013 forcefield, with a dt of .5fs 
emtol of 1.0 and niter of 150
using the V-rescale thermostat and Berendsen pressure coupling while my systems 
cell shape relaxes
as a continuation from position restrained NVT then NPT ensembles. The starting 
structures were minimized
in vacuum, then solvated and minimized once again prior to the posres 
equilibration.



Such a short dt and strict niter should not be necessary in practice.  The
failure of SCF to converge/LINCS warnings is what we typically refer to as
polarization catastrophe, so your system is on the brink of instability.  This
is one of the inherent problems of SCF in polarizable systems; it often fails to
converge and leaves the system potentially unstable.  The reflective hardwall is
much more reliable (and faster).  If the instability is happening in your
equilibration, that may be OK but it is something you should try to troubleshoot
to make sure there's nothing else going wrong.

-Justin

--



Got it. I have been spending some time investigating the issue i’m having and
after reading shellfc.cpp I was pretty confident the issue was with SCF not 
converging,
and so my niter and dt were an attempt at looking into that.

The workflow i’ve been trying to use is…
EM -> Solvate -> EM -> posres NVT V-rescale -> posres berendsen NPT isotropic 1bar 
w/ V-rescale tcoupl ->
berendsen NPT semi-isotropic various pressures w/ V-rescale tcoupl

then once my cell shape has reached an equilibrium I finally switch to NH 
thermostat and PR barostat for
the production run.

If I switch to employing the hardwall (and the lagrangian dynamics for drudes) 
then I understand it is not
compatible yet with NPT ensembles. So, if I change my work flow as follows 
would it be appropriate still?

EM->Solvate->EM->posre NPT isotropic 1 bar w/ V-rescale tcoupl->NPT 
semi-isotropic varying pressures
w V-rescale tcoupl until cell shape is equilibrated using PR barostat, then 
switch to NVT without pcoupl
to use the hardwall during my production run?

For some reason, i’ve got this idea that I need to be tcoupling and pcoupling 
during my production runs
so i’ve been apprehensive to do this.



If you want an NPT ensemble during dynamics you're going to have to use NAMD, 
CHARMM, or OpenMM.  I haven't coded the barostat yet (fixing the DD bugs has 
been more important).  You can equilibrate with SCF under NPT and get a suitable 
density, then switch to NVT, but your use of semi-isotropic coupling suggests a 
membrane system?  In that case, I would not use NVT during production as you 
will be simulating a constant area, which may not be appropriate.


-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] How to extend simulation?

[Justin Lemkul]

On 4/3/17 2:20 PM, ZHANG Cheng wrote:

Thank you. So if the below is correct, and it will run for 100 ns?


convert-tpr -s previous.tpr -extend 10 -o next.tpr
gmx mdrun -deffnm next -cpi previous.cpt



Have you tried it?

-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] CHARMM27 hates my DMPC

[Vytautas Rakeviius]

Hello,
I have my system with DMPC bilayers in pdb and try to convert it into GROMACS 
input. Because system is with lipids I think chose CHARMM27 ff. But still I get 
lots of warnings like that: 

https://pastebin.com/K8dHKkUi
Also I add my DMPC pdb as example. What should I do? Rename all my DMPC 
atoms?Thanks for all suggestions.


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[gmx-users] .mdp file for Enthalpy of Vaporization calculation

[Matteo Busato]

Goodmorning to everyone,


I'm writing here because I'm trying to perform a calculation about the Enthalpy 
of Vaporization of a system with 434 molecules of an ionic liquid. I've already 
read all the previous posts in the forum about this subject and it has come 
clear to me how to perform the calculation, however I'm having problems with my 
.mdp file when trying to perform the NVT equilibration.

I've read that for such calculation cutoffs must be set = 0 and pbc=none, 
however with such parameters I'm forced to use cutoff-scheme=group instead of 
Verlet, so the first problem is that 'group' is not configured for GPU 
acceleration and I can use just 1 MPI rank (which slows the job time a lot). Is 
there a way to perform this calculation with Verlet?

The second problem is that if I set rvdw=0, gromacs gives me an error saying 
that (obviously), vdw-switch must be < rvdw. How can I solve this issue?

I'll post the mdp I'm using here. Thank you in advance.


; Run control
integrator   = sd   ; Langevin dynamics
tinit= 0
dt   = 0.001
nsteps   = 100; 1000 ps
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= group
nstlist  = 0
ns_type  = grid
pbc  = no
rlist= 0
; Electrostatics
coulombtype  = cutoff
rcoulomb = 0
; van der Waals
vdwtype  = cutoff
vdw-modifier = potential-switch
rvdw = 0
rvdw-switch  =0
; 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= 298.15
; Pressure coupling is off for NVT
Pcoupl   = No
tau_p= 0.5
compressibility  = 4.5e-05
ref_p= 1.0
; Generate velocities to start
gen_vel  = yes
gen_temp = 300
gen_seed = -1
; options for bonds
constraints  = h-bonds  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Do not constrain the starting configuration
continuation = no
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 12
dispcorr=no


Matteo Busato
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[gmx-users] Pulling/restraints along the radius of gyration

[Jochen Hub]

Hi Gromacs users,

we have written a little Gromacs extension that allows you to apply 
harmonic restraints along the radius of gyration of a group of atoms 
(such as a protein). If you want to use it, here are some more details:


http://cmb.bio.uni-goettingen.de/rg_pulling.html

Cheers,
Jochen

--
---
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
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[gmx-users] No data on Pullf and Pullx files after restart

[Souparno Adhikary]

Hello,

I restarted my umbrella sampling simulations using the tpbconv command. I
used the -vel option in the command. It ran successfully. After that, when
I am running the new simulations, pullf and pullx files are created for
each sample but no data gets written in them.

I am absolutely clueless how to solve this. Can you please help?

Thanks in advance.

Best regards,

Souparno
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Re: [gmx-users] gmx insert-molecules - molecules "sticking out of the box"

[Magnus Lundborg]

Hi,

Assuming that you are using a periodic box it shouldn't matter that the
molecules are placed crossing the edges - that just means the rest will be
on the opposing side of the box when you simulate. If you wish to visualize
the system you could experiment with the -pbc options of the trjconv tool.

Cheers,

Magnus

Den 4 apr. 2017 10:03 skrev "Jernej Zidar" :

> Hi,
>
> I am using 'gmx insert-molecules' to insert ten rather large polymer
> molecules into a 16x16x16 nm box. The problem is that the utility inserts
> the molecules randomly (which is good) in way that leaves the polymer
> molecules sticking outside the defined box and leaving lots of space empty.
>
> The manual lists a number of potential useful options under the switch
> "-selrpos" but the manual says nothing about what do the options do.
>
> How to instruct 'gmx insert-molecules' to keep the inserted molecules
> whole?
>
> Thanks,
> Jernej
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[gmx-users] gmx insert-molecules - molecules "sticking out of the box"

[Jernej Zidar]

Hi,

I am using 'gmx insert-molecules' to insert ten rather large polymer
molecules into a 16x16x16 nm box. The problem is that the utility inserts
the molecules randomly (which is good) in way that leaves the polymer
molecules sticking outside the defined box and leaving lots of space empty.

The manual lists a number of potential useful options under the switch
"-selrpos" but the manual says nothing about what do the options do.

How to instruct 'gmx insert-molecules' to keep the inserted molecules whole?

Thanks,
Jernej
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[gmx-users] gmx insert_molecules problem

[吴萌]

Hi All,

  I am running a membrane protein MD simulation with Gromacs 5.1.4. I want to 
add some substrate molecules(acetate) to my system, and I used this command:
  "gmx insert_molecules -f ###.pdb(include the ptotein, POPC, etc.) -ci act.pdb 
-o ###.pdb -nmol 48 -box 6.7 6.7 8.1 -try 500 -rot xyz",
  but then I found many acetate molecules are put out of the system in the out 
.pdb.
  Is that normol or wouldl affect the later MD process? If so, how can I fix it.
  Any suggestions would be greatly appreciated. Thank you in advance!

All the best,
Wu Meng
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