[gmx-users] (no subject)

[Shivangi Agarwal]

Dear all gromacs users

i have to define a new residue, i have added it in *residuetype.dat* file.
but still getting error: "residue type not found".
Kindly suggest
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Re: [gmx-users] Atom types comparison between CGenFF and Charm36FF

[Justin Lemkul]

On 6/27/17 3:27 PM, Mohsen Ramezanpour wrote:

Dear Gromacs Users,

I am trying to parameterize a molecule in Charmm36FF.

As part of this molecule, there is a "neutral trimethylamine nitrogen" and
its protonated case. i.e. C-N-C(2) and C-N(H)-C(2), respectively.

To have some idea about the appropriate atom types, I first used the
GAAMP server.

Here are the assigned atom types by GAAMP (based on CGenFF force field):


*For Neutral case:*
NG301 for N,
CG3AM0 for two methyl group connected to the N, i.e for bolded Carbons in
C-N-*C(2).*
HGA3 for each Hydrogen atom in CG3AM0 methyl groups,
CG321 for the carbon atom connecting the NC(2) to the rest of molecule.
i.e. for bolded Carbon in *C*-N-C(2),
and HGA2 for the Hydrogen atoms connected to CG321.
###

*For Protonated case:*
NG3P1 for N,
CG334 for two methyl group connected to the N, i.e for bolded Carbons in
C-N(H)-*C(2).*
HGA3 for each Hydrogen atom in CG334 methyl groups,
CG324 for the carbon atom connecting the NC(2) to the rest of molecule.
i.e. for bolded Carbon in *C*-N(H)-C(2),
and HGA2 for the Hydrogen atoms connected to CG321.


Now, I want to find the best equivalent atom type in Charmm36FF for each
case.

For the protonated case, I think it is easier as it is something between PE
and PC lipid headgroups. For the neutral case, however, it is difficult to
find similar atom types in Charmm36.

My approach was to check the LJ and bonded parameters for the assigned atom
types (which are in CGenFF) and find the atom types in Charmm36 with the
exact same values. Although possible for some cases, but there are many
problems with this approach:

1) the exact values are not found in Charmm36FF.
2) If it is found, there are a lot of parameters missing in the Charmm36FF
force field. Not all the bonds, angles, and dihedrals are defined in
Charmm36FF.

Thanks in advance for any comment or suggestion.



The "G" in CGenFF is for "general," which means the parameters are not 
necessarily the same as the parent CHARMM force field, and are subsequently a 
compromise between being highly optimized (e.g. CHARMM36) and being broadly 
applicable (general) such that the types can be used across different molecules.


If you want to parametrize something for CHARMM, e.g. to be merged into a larger 
molecule, you're wasting your time with trying to generate a CGenFF topology and 
try to find exact matches in CHARMM36.  By definition, you won't.  If your goal 
is a CHARMM topology, then start from existing CHARMM atom types, import charges 
by analogy, and do a full parametrization procedure (well described in numerous 
places in the literature).


-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] adding a custom residue with an itp file

[Justin Lemkul]

On 6/27/17 12:32 PM, Jose Borreguero wrote:

Dear Gromacs users,

I have created an include topology file (sil.itp) for a silica crystal, but
the instructions in
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
leave me with a couple of unclear points. Please help!

1. This "residue" is not of type 'Protein' or 'DNA', so can I just create a
new type in file residuestypes.dat? Something like "SIL Silica"? Do I
actually have to declare this molecule within residuestypes.dat?

2. All the bonding info is already in the sil.itp file I just created, but
do I still have to include this residue in file aminoacids.rtp?



You only need aminoacids.rtp and residuetypes.dat if you're running pdb2gmx. 
You already have a topology, so there is no purpose to running 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

==
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Re: [gmx-users] Doubt about Free Energy control Minimization

[Justin Lemkul]

On 6/27/17 7:43 AM, Varvdekar Bhagyesh Rajendra wrote:

Dear Justin,

When the system is minimized with full interactions with no free energy code, I 
see no warnings and the systems is minimized properly.

However, when the free energy code is added with couple-intramol = no, I 
encounter the said warning, but still the system can be minimized ignoring the 
warning.

When the free energy code is added with couple-intramol = yes, there's no 
warning, but the system is again well minimized.



You may need several rounds of energy minimization to get a stable result.  Your 
final minimization and equilibration should be done under the 
conditions/settings that make the most sense for you to model.


-Justin


I would like to learn if its reasonable to ignore the warning in the case where 
couple-intramol = no, since I am dealing with a peptide and intramolecular 
interactions can suppress the intermolecular interactions.

I intend to perform normal-mode calculations on the resulting intermediates 
which are divergent from the Binding energy simulations requiring convergence. 
Hence, I presume there shouldn't be much complication in this case. I 
understand the approach seems quite outlandish, but still I aspire to execute 
the same. Any opinions and/or suggestions in this procedure will be greatly 
helpful.

Many thanks,

Bhagyesh.


- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Tuesday, June 27, 2017 6:42:33 PM
Subject: Re: [gmx-users] Doubt about Free Energy control Minimization

On 6/26/17 9:09 AM, Varvdekar Bhagyesh Rajendra wrote:

Dear Justin,

I have encountered the following warning when I used the following code to 
minimize my protein-ligand system when the interaction potential energy between 
the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 0.2, 0.1.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp

Warning: 1-4 interaction between 2263 and 2298 at distance 1.004 which is 
larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size


I suppose this error is due to setting couple-intramol = no. When it is set to 
yes, the warning vanishes.

But, this is my desired setting since, I do not intend to scale the intra molecular 
interactions even though the ligand is a peptide. Is it reasonable to ignore the warning. 
If not , how can it affect my resulting structure ? And are all such interaction 
"ignored for the rest of the simulation" ?



So the system is unstable.  Try minimizing with full interactions before doing
anything funny with scaling.  And I repeat my caution to you that trying to do
an alchemical transformation of a peptide is a very unwise choice.  You'll never
get the simulations to converge in a practical amount of time.

-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] gmx spatial

[Dallas Warren]

The values for the isosurface are a probability, just like for an RDF,
so negative values don't make any sense.

Visualise the trajectory you are analysing to see how the solute moves
around, and get a visual idea of if the SDF generated is consistent
with what you are seeing.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 28 June 2017 at 01:45, Valerio Ferrario  wrote:
> Dear Users,
>
> I am trying to use the gmx spatial tool in order to understand how a solute
> interact with the protein. I performed the calculation following all the
> instructions (including the 2 trjconv steps). The trajectory obtained looks
> fine, and I calculated the sdf with the following command:
>
> gmx_mpi spatial -f CALBtrjvonv2.xtc -s CALBMpr-1.tpr -n X.ndx
>
> and selecting the protein and an atom of my solute molecules (in the index)
>
> but when I open the grid.cube file with vmd and I visualize it as
> isosurface I have the density function even within the protein core... I
> thought that the density should be just around the protein (in this case).
> Moreover I have just positive values for the isosurface, is that normal? Am
> I doing something wrong?
>
> Thanks a lot,
> Valerio Ferrario
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Re: [gmx-users] Number of Contacts

[Dallas Warren]

First thing you should do when asking for help, is specify exactly
what you have have done (that includes the command line and output),
and then why it is "wrong result".
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 28 June 2017 at 01:27, Sundari chaudhary  wrote:
> Dear all,
>
> I want to calculate the number of inter-peptide and intra-peptide
> side-chain–side-chain contacts and the criteria to form a contact is that:
> the distance between the centers of mass of two residues is less than a
> specified distance. I tried gmx mindist and gmx distance command lines but
> i got wrong results.
>
> Please suggest me right command line to do this analysis.
>
>
> Thank you!
>
> Sundari
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[gmx-users] Atom types comparison between CGenFF and Charm36FF

[Mohsen Ramezanpour]

Dear Gromacs Users,

I am trying to parameterize a molecule in Charmm36FF.

As part of this molecule, there is a "neutral trimethylamine nitrogen" and
its protonated case. i.e. C-N-C(2) and C-N(H)-C(2), respectively.

To have some idea about the appropriate atom types, I first used the
GAAMP server.

Here are the assigned atom types by GAAMP (based on CGenFF force field):


*For Neutral case:*
NG301 for N,
CG3AM0 for two methyl group connected to the N, i.e for bolded Carbons in
C-N-*C(2).*
HGA3 for each Hydrogen atom in CG3AM0 methyl groups,
CG321 for the carbon atom connecting the NC(2) to the rest of molecule.
i.e. for bolded Carbon in *C*-N-C(2),
and HGA2 for the Hydrogen atoms connected to CG321.
###

*For Protonated case:*
NG3P1 for N,
CG334 for two methyl group connected to the N, i.e for bolded Carbons in
C-N(H)-*C(2).*
HGA3 for each Hydrogen atom in CG334 methyl groups,
CG324 for the carbon atom connecting the NC(2) to the rest of molecule.
i.e. for bolded Carbon in *C*-N(H)-C(2),
and HGA2 for the Hydrogen atoms connected to CG321.


Now, I want to find the best equivalent atom type in Charmm36FF for each
case.

For the protonated case, I think it is easier as it is something between PE
and PC lipid headgroups. For the neutral case, however, it is difficult to
find similar atom types in Charmm36.

My approach was to check the LJ and bonded parameters for the assigned atom
types (which are in CGenFF) and find the atom types in Charmm36 with the
exact same values. Although possible for some cases, but there are many
problems with this approach:

1) the exact values are not found in Charmm36FF.
2) If it is found, there are a lot of parameters missing in the Charmm36FF
force field. Not all the bonds, angles, and dihedrals are defined in
Charmm36FF.

Thanks in advance for any comment or suggestion.

Cheers,
Mohsen





-- 
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Re: [gmx-users] By using the Gromacs to simulate Raman spectrum

[Alex]

There's sort of no point in doing that, or, rather doing the simulations.
Given the type of interactions most of biophysics forcefields have
(harmonic springs), you can in fact calculate everything without any
simulations. That is, if you never use constrained bonds. If you do use
constrained bonds, your frequencies will approach infinity, because the
resulting bond stiffness is very high. A relatively decent way of doing
vibrational analysis for organics is with DFT, e.g. with Gaussian, which
has provisions for determining the frequencies. You probably will not be
able to actually plot Raman spectra, but instead you could simulate the
peaks observed in Raman spectra.

Alex

On Tue, Jun 27, 2017 at 12:36 PM, lu lu  wrote:

> Greeting,
>
>   Hello, I am a new beginner for Gromacs. Our group is trying to simulate
> Raman spectrum for a variety of small organic molecules, like amino acid
> and ribonucleic acid.
>
>  I was planning to use both GAMESS and Gromacs to simulate the Raman
> Spectrum for tyrosine. My plan was simulated the single tyrosine molecule
> by GAMESS and use the Gromacs to simulate clustered tyrosine behavior and
> extract the Raman spectrum from it. However, after I did some research
> online, I found out that, almost no one uses Gromacs to do the vibrational
> spectrum. It seems like Gromacs is mainly used for simulating the
> interaction dynamics between small molecules like nanoparticles interacting
> with lipid membrane.
>
>  So, my question is, it is possible to use Gromacs to do the simulation for
> Raman spectrum? If so, would anyone show a direction for how to get it?
>
>  Thank you for your guys helping,
>
>  Best Regards,
>  Lu
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>
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[gmx-users] By using the Gromacs to simulate Raman spectrum

[lu lu]

Greeting,

  Hello, I am a new beginner for Gromacs. Our group is trying to simulate
Raman spectrum for a variety of small organic molecules, like amino acid
and ribonucleic acid.

 I was planning to use both GAMESS and Gromacs to simulate the Raman
Spectrum for tyrosine. My plan was simulated the single tyrosine molecule
by GAMESS and use the Gromacs to simulate clustered tyrosine behavior and
extract the Raman spectrum from it. However, after I did some research
online, I found out that, almost no one uses Gromacs to do the vibrational
spectrum. It seems like Gromacs is mainly used for simulating the
interaction dynamics between small molecules like nanoparticles interacting
with lipid membrane.

 So, my question is, it is possible to use Gromacs to do the simulation for
Raman spectrum? If so, would anyone show a direction for how to get it?

 Thank you for your guys helping,

 Best Regards,
 Lu
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[gmx-users] adding a custom residue with an itp file

[Jose Borreguero]

Dear Gromacs users,

I have created an include topology file (sil.itp) for a silica crystal, but
the instructions in
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
leave me with a couple of unclear points. Please help!

1. This "residue" is not of type 'Protein' or 'DNA', so can I just create a
new type in file residuestypes.dat? Something like "SIL Silica"? Do I
actually have to declare this molecule within residuestypes.dat?

2. All the bonding info is already in the sil.itp file I just created, but
do I still have to include this residue in file aminoacids.rtp?

Best,
Jose
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[gmx-users] gmx spatial

[Valerio Ferrario]

Dear Users,

I am trying to use the gmx spatial tool in order to understand how a solute
interact with the protein. I performed the calculation following all the
instructions (including the 2 trjconv steps). The trajectory obtained looks
fine, and I calculated the sdf with the following command:

gmx_mpi spatial -f CALBtrjvonv2.xtc -s CALBMpr-1.tpr -n X.ndx

and selecting the protein and an atom of my solute molecules (in the index)

but when I open the grid.cube file with vmd and I visualize it as
isosurface I have the density function even within the protein core... I
thought that the density should be just around the protein (in this case).
Moreover I have just positive values for the isosurface, is that normal? Am
I doing something wrong?

Thanks a lot,
Valerio Ferrario
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[gmx-users] Number of Contacts

[Sundari chaudhary]

Dear all,

I want to calculate the number of inter-peptide and intra-peptide
side-chain–side-chain contacts and the criteria to form a contact is that:
the distance between the centers of mass of two residues is less than a
specified distance. I tried gmx mindist and gmx distance command lines but
i got wrong results.

Please suggest me right command line to do this analysis.


Thank you!

Sundari
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Re: [gmx-users] Simulation ended prematurely, no performance report will be written- Minimization

[Peter Kroon]

That means your system is minimized. Or at least as minimized as it's
going to get starting from this structure.


Peter


On 27-06-17 16:02, Alex Mathew wrote:
> Dear all,
>
> I'm trying to minimise the CGMD system and end up with an error Steepest
> Descents converged to machine precision in XX steps,
> but did not reach the requested Fmax < XX.  I tried double precision and
> feed the *.gro file as the initial structure but the result was same. There
> were no overlaping in the *.gro file , I have attached the *.log file in
> the below link.
>
> ​​
> https://drive.google.com/file/d/0Bzs8lO6WJxD9cFhmWTQwRXdtN2c/view?usp=sharing


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[gmx-users] Simulation ended prematurely, no performance report will be written- Minimization

[Alex Mathew]

Dear all,

I'm trying to minimise the CGMD system and end up with an error Steepest
Descents converged to machine precision in XX steps,
but did not reach the requested Fmax < XX.  I tried double precision and
feed the *.gro file as the initial structure but the result was same. There
were no overlaping in the *.gro file , I have attached the *.log file in
the below link.

​​
https://drive.google.com/file/d/0Bzs8lO6WJxD9cFhmWTQwRXdtN2c/view?usp=sharing
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Re: [gmx-users] Doubt about Free Energy control Minimization

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

When the system is minimized with full interactions with no free energy code, I 
see no warnings and the systems is minimized properly. 

However, when the free energy code is added with couple-intramol = no, I 
encounter the said warning, but still the system can be minimized ignoring the 
warning.

When the free energy code is added with couple-intramol = yes, there's no 
warning, but the system is again well minimized.

I would like to learn if its reasonable to ignore the warning in the case where 
couple-intramol = no, since I am dealing with a peptide and intramolecular 
interactions can suppress the intermolecular interactions.

I intend to perform normal-mode calculations on the resulting intermediates 
which are divergent from the Binding energy simulations requiring convergence. 
Hence, I presume there shouldn't be much complication in this case. I 
understand the approach seems quite outlandish, but still I aspire to execute 
the same. Any opinions and/or suggestions in this procedure will be greatly 
helpful.

Many thanks,

Bhagyesh.


- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Tuesday, June 27, 2017 6:42:33 PM
Subject: Re: [gmx-users] Doubt about Free Energy control Minimization

On 6/26/17 9:09 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> I have encountered the following warning when I used the following code to 
> minimize my protein-ligand system when the interaction potential energy 
> between the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 0.2, 
> 0.1.
> 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp
> 
> Warning: 1-4 interaction between 2263 and 2298 at distance 1.004 which is 
> larger than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> 
> 
> I suppose this error is due to setting couple-intramol = no. When it is set 
> to yes, the warning vanishes.
> 
> But, this is my desired setting since, I do not intend to scale the intra 
> molecular interactions even though the ligand is a peptide. Is it reasonable 
> to ignore the warning. If not , how can it affect my resulting structure ? 
> And are all such interaction "ignored for the rest of the simulation" ?
> 

So the system is unstable.  Try minimizing with full interactions before doing 
anything funny with scaling.  And I repeat my caution to you that trying to do 
an alchemical transformation of a peptide is a very unwise choice.  You'll 
never 
get the simulations to converge in a practical amount of time.

-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] DNA splitting in simulations

[Justin Lemkul]

On 6/27/17 7:11 AM, Sergio Manzetti wrote:

Thanks for the funny message, but I dont think this is recollection of 
imaginary character: just tried with one Tcppl group (SOL) :

Fatal error:
1435 atoms are not part of any of the T-Coupling groups
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors




If you're only trying to couple the water (SOL) to a thermostat, then naturally 
grompp is going to tell you that you're doing something that is not sensible. 
It is *not* telling you "you need to set every type of molecule to its own 
group," it is telling you that what you're doing is fundamentally unphysical by 
coupling some atoms but not all.  Normally one would set "System" or at most two 
separate groups for the solute (DNA) and the combined solvent (a merged group of 
water and ions, created with make_ndx).  I know at least my tutorial walks you 
through this.


-Justin





Sergio Manzetti

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

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



From: "Justin Lemkul" 
To: "gmx-users" 
Sent: Tuesday, June 27, 2017 3:11:15 PM
Subject: Re: [gmx-users] DNA splitting in simulations

On 6/27/17 7:05 AM, Sergio Manzetti wrote:

Jose, thanks for the DPOSRE. About the multiple tcoupling, as mentioned in the 
email, grompp wanted equal number of tcouplings as groups in the top file.



That's not true and what you're doing is not sensible. If you're having a
problem, please provide an exact error message from grompp, not what's filtered
through your recollection :)

-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] DNA splitting in simulations

[Sergio Manzetti]

Thanks for the funny message, but I dont think this is recollection of 
imaginary character: just tried with one Tcppl group (SOL) : 

Fatal error: 
1435 atoms are not part of any of the T-Coupling groups 
For more information and tips for troubleshooting, please check the GROMACS 
website at http://www.gromacs.org/Documentation/Errors 





Sergio Manzetti 

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

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



From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Tuesday, June 27, 2017 3:11:15 PM 
Subject: Re: [gmx-users] DNA splitting in simulations 

On 6/27/17 7:05 AM, Sergio Manzetti wrote: 
> Jose, thanks for the DPOSRE. About the multiple tcoupling, as mentioned in 
> the email, grompp wanted equal number of tcouplings as groups in the top 
> file. 
> 

That's not true and what you're doing is not sensible. If you're having a 
problem, please provide an exact error message from grompp, not what's filtered 
through your recollection :) 

-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] Doubt about Free Energy control Minimization

[Justin Lemkul]

On 6/26/17 9:09 AM, Varvdekar Bhagyesh Rajendra wrote:

Dear Justin,

I have encountered the following warning when I used the following code to 
minimize my protein-ligand system when the interaction potential energy between 
the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 0.2, 0.1.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp

Warning: 1-4 interaction between 2263 and 2298 at distance 1.004 which is 
larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size


I suppose this error is due to setting couple-intramol = no. When it is set to 
yes, the warning vanishes.

But, this is my desired setting since, I do not intend to scale the intra molecular 
interactions even though the ligand is a peptide. Is it reasonable to ignore the warning. 
If not , how can it affect my resulting structure ? And are all such interaction 
"ignored for the rest of the simulation" ?



So the system is unstable.  Try minimizing with full interactions before doing 
anything funny with scaling.  And I repeat my caution to you that trying to do 
an alchemical transformation of a peptide is a very unwise choice.  You'll never 
get the simulations to converge in a practical amount of time.


-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] DNA splitting in simulations

[Justin Lemkul]

On 6/27/17 7:05 AM, Sergio Manzetti wrote:

Jose, thanks for the DPOSRE. About the multiple tcoupling, as mentioned in the 
email, grompp wanted equal number of tcouplings as groups in the top file.



That's not true and what you're doing is not sensible.  If you're having a 
problem, please provide an exact error message from grompp, not what's filtered 
through your recollection :)


-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] DNA splitting in simulations

[Sergio Manzetti]

Jose, thanks for the DPOSRE. About the multiple tcoupling, as mentioned in the 
email, grompp wanted equal number of tcouplings as groups in the top file. 


Sergio Manzetti 

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

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



From: "João Henriques"  
To: "gmx-users"  
Sent: Tuesday, June 27, 2017 11:51:17 AM 
Subject: Re: [gmx-users] DNA splitting in simulations 

Hi! 

Your mdp file doesn't tell the engine to apply the restraints during the 
simulation... You need to specify: 
define = -DPOSRES 

Also, didn't Justin already warn you about using separate temperature 
couplings for every component of your system? 

Please check the "What Not To Do" section under: 
http://www.gromacs.org/Documentation/Terminology/Thermostats 

Best regards, 
João 

On Tue, Jun 27, 2017 at 11:22 AM, Sergio Manzetti < 
sergio.manze...@fjordforsk.no> wrote: 

> Hi, I Have run a DNA piece in a box of 7 7 7 , with NaCl ions 
> neutralizing, as discussed earlier. The simulation went fine without any 
> errors, however it turns out the DNA strands separate. The position 
> restraints made by pdb2gmx using the AMBERDB ISTN ff are not working ? 
> 
> This is the posres file: 
> In this topology include file, you will find position restraint 
> ; entries for all the heavy atoms in your original pdb file. 
> ; This means that all the protons which were added by pdb2gmx are 
> ; not restrained. 
> 
> [ position_restraints ] 
> ; atom type fx fy fz 
> 1 1 1000 1000 1000 
> 3 1 1000 1000 1000 
> 6 1 1000 1000 1000 
> 8 1 1000 1000 1000 
> 9 1 1000 1000 1000 
> 11 1 1000 1000 1000 
> 12 1 1000 1000 1000 
> 14 1 1000 1000 1000 
> 15 1 1000 1. 
> 
> 
> and here is the simulation mdp. 
> 
> 
> 
> 
> itle = DNA in water stabilization 
> cpp = /lib/cpp 
> include = -I../top 
> define = 
> integrator = md 
> dt = 0.002 
> nsteps = 500 
> nstxout = 5000 
> nstvout = 5000 
> nstlog = 5000 
> nstenergy = 300 
> nstxout-compressed = 300 
> compressed-x-grps = DNA SOL NA CL 
> energygrps = DNA SOL NA CL 
> nstlist = 20 
> ns-type = grid 
> rlist = 0.8 
> coulombtype = PME 
> rcoulomb = 0.8 
> rvdw = 0.8 
> tcoupl = V-Rescale 
> tc-grps = SOL DNA NA CL 
> tau-t = 0.1 0.1 0.1 0.1 
> 
> 
> 
> Note that GMX gromp wanted 4 groups at tc_grps and tau_t, otherwise it 
> wouldn't proceed. 
> 
> 
> Thanks! 
> 
> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ 
> | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ 
> http://www.phap.no/ | FAP ] 
> 
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Re: [gmx-users] CGMD with cut-off Verlet? production run stage

[Peter Kroon]

Hi,


read the paper I sent earlier if you want to be sure. There's also a
version that uses RF or PME, but they're (a bit) slower.

See
http://cgmartini.nl/index.php/force-field-parameters/input-parameters
for the full list.


Peter


On 27-06-17 12:57, Mark Abraham wrote:
> Hi,
>
> You should use force fields the way their designers intended them to be
> used (or how they use them now). Most force fields used with GROMACS should
> not be used with plain Coulomb, hence the note.
>
> Mark
>
> On Tue, Jun 27, 2017 at 12:49 PM Alex Mathew  wrote:
>
>> Hi,
>>
>> Based on this mdp
>> http://cgmartini.nl/images/parameters/exampleMDP/martini_v2.x_new.mdp
>>
>> i got NOTE
>>
>>
>>   You are using a plain Coulomb cut-off, which might produce artifacts.
>>   You might want to consider using PME electrostatics.
>>
>> Is this something i need to consider or just ignore?
>> --
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Re: [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

[Mark Abraham]

Hi,

You need to understand how AMBER uses the contents of the prm file, and how
to produce suitable .rtp and atom type entries for use with GROMACS. This
will mean some spending some quality time with the documentation. That's
one reason that such simulations are not a good idea for someone learning
how to do molecular simulations.

Mark

On Tue, Jun 27, 2017 at 6:06 AM Rana Rehan Khalid 
wrote:

> Hi
> I have ff of heme fe---o2  some one use it before these are amber heme ff
> he use amber 99sb and this heme ff in his md  simulation  but he done his
> work in amber. Can you guide me that how I can use this heme ff of amber in
> combination with amber99sb  at number 6 position in gromacs
>
> On Jun 14, 2017 4:55 PM, "Justin Lemkul"  wrote:
>
>
>
> On 6/14/17 12:25 AM, Rana Rehan Khalid wrote:
>
> > Hi
> > I have read the chapter 5 of manual but i am confuse how can i add
> residue
> > into heme atom of .rtp ff
> > this is the coordinate due to which error come
> >
> > HETATM 1529  O01 HEM   187   3.996  19.101  70.594  0.00
> > 0.00   O
> >
> > kindly guide me how i can make changes in the rtp file and .atp so that
> > this error remove
> > here is the heme rtp part of my selected ff where i can add O01 and also
> > tell me these 4 column and these values and tell me which value i add for
> > O01 like (FE FE 0.4 0 )
> >
>
> You should refer back to the manual if the contents of these files are not
> clear.  You're seeking to introduce new parameters for an oxygen-bound form
> of heme; this may require very complex parametrization work.  Modifying an
> .rtp file is trivial; it's just text.  Putting realistic parameters into it
> is a whole other matter.  Check the literature for any existing efforts to
> avoid duplicated work.
>
> -Justin
>
>
> [ HEME ]
> >   [ atoms ]
> > FEFE 0.4 0
> > NANR-0.1 0
> > NBNR-0.1 0
> > NCNR-0.1 0
> > NDNR-0.1 0
> >CHA C-0.1 1
> >HHAHC 0.1 1
> >C1A C 0.0 2
> >C2A C 0.0 2
> >C3A C 0.0 2
> >C4A C 0.0 2
> >CMA   CH3 0.0 3
> >CAA   CH2 0.0 4
> >CBA   CH2 0.0 4
> >CGA C 0.27000 5
> >O1AOM-0.63500 5
> >O2AOM-0.63500 5
> >CHB C-0.1 6
> >HHBHC 0.1 6
> >C1B C 0.0 7
> >C2B C 0.0 7
> >C3B C 0.0 7
> >C4B C 0.0 7
> >CMB   CH3 0.0 8
> >CAB   CR1 0.0 9
> >CBB   CH2 0.0 9
> >CHC C-0.110
> >HHCHC 0.110
> >C1C C 0.011
> >C2C C 0.011
> >C3C C 0.011
> >C4C C 0.011
> >CMC   CH3 0.012
> >CAC   CR1 0.013
> >CBC   CH2 0.013
> >CHD C-0.114
> >HHDHC 0.114
> >C1D C 0.015
> >C2D C 0.015
> >C3D C 0.015
> >C4D C 0.015
> >CMD   CH3 0.016
> >CAD   CH2 0.017
> >CBD   CH2 0.017
> >CGD C 0.2700018
> >O1DOM-0.6350018
> >O2DOM-0.6350018
> >
> > thanks
> >
> >
> --
> ==
>
> 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] Should the peptide be centered initially in the box if we want to calculate its diffusion later?

[Mark Abraham]

Hi,

There's no center of a periodic cell, so wherever you place it originally
is arbitrary. You get restraints only if you choose to have them in your
topology.

Mark

On Tue, Jun 27, 2017 at 9:00 AM Apramita Chand 
wrote:

> Dear All,
> Using g_editconf, I am centering the peptide in the box initially. During
> equilibration, I'm gradually releasing position restraints. I want the
> peptide to be free to move around so that I might calculate its diffusion
> constant.
> In that case, will centering using -c option restrain its motion ?
>
>
> yours sincerely
> Apramita
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Re: [gmx-users] CGMD with cut-off Verlet? production run stage

[Mark Abraham]

Hi,

You should use force fields the way their designers intended them to be
used (or how they use them now). Most force fields used with GROMACS should
not be used with plain Coulomb, hence the note.

Mark

On Tue, Jun 27, 2017 at 12:49 PM Alex Mathew  wrote:

> Hi,
>
> Based on this mdp
> http://cgmartini.nl/images/parameters/exampleMDP/martini_v2.x_new.mdp
>
> i got NOTE
>
>
>   You are using a plain Coulomb cut-off, which might produce artifacts.
>   You might want to consider using PME electrostatics.
>
> Is this something i need to consider or just ignore?
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Re: [gmx-users] Simulations stop running after reaching specific time step

[Mark Abraham]

Hi,

Most likely a network file system that has dropped out. These tend to
report to the application that the data was written (but actually only to a
memory buffer), so it continues on. Then when there's nowhere for the
memory buffer to be written, there's nobody to report that to...

Mark

On Tue, Jun 27, 2017 at 9:44 AM Shobha Sharma 
wrote:

> Hello,
>
> I am submitting few simulations, after providing the wall time enough to
> finish the jobs. But after reaching a certain time step, in case of all
> jobs, the output files are not written beyond that time step.
>
> For example if I check my .log file, using 'tail -f md.log'  I find that it
> is not writing anything even though job is running. It utilizes whole wall
> time given and ends without writing any further time steps.
> In the end it does not even write about any problem faced. Job ends due to
> end of wall time.
>
> What might be the reason behind this?
>
> --
> Thanks and Regards,
> Shobha
> --
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[gmx-users] Difference between semi isotropic coupling and surface tension option

[Ali Shomali]

Dear all Gromacs users

I'm simulating a monolayer at water/vacuum interface with Gromacs and I'm
studying surface tension and area per lipid variations. the problem that is
very confusing me on this subject is that when I use semiisotropic option
to impose a negative lateral pressure and so a specific surface tension ,
my final area per lipid is very different from surface tension option but
when I use my energy files, both of them (surface tension or semiisotropic
output) are resulted in a very same  surface tensions.so how is it possible
that the same surface tension gives different area per lipids? if the
procedures are different, which one is more accurate?
I appreciate your kind and helpful advises.

Ali
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[gmx-users] CGMD with cut-off Verlet? production run stage

[Alex Mathew]

Hi,

Based on this mdp
http://cgmartini.nl/images/parameters/exampleMDP/martini_v2.x_new.mdp

i got NOTE


  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.

Is this something i need to consider or just ignore?
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Re: [gmx-users] Should the peptide be centered initially in the box if we want to calculate its diffusion later?

[Nikhil Maroli]

Hi Apramita,

Up to my knowledge, It is not necessary to keep the peptide at the centre
due to the periodicity you can have 'continues' motion throughout the
simulation. But, it is always better to keep it in convenient positions to
avoid any artefacts. Further, I don't have any idea about your simulation
system, whether it contains lipid layers or any other proteins and what
kind of motions/diffusions your expecting.
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Re: [gmx-users] DNA splitting in simulations

[João Henriques]

Hi!

Your mdp file doesn't tell the engine to apply the restraints during the
simulation... You need to specify:
define = -DPOSRES

Also, didn't Justin already warn you about using separate temperature
couplings for every component of your system?

Please check the "What Not To Do" section under:
http://www.gromacs.org/Documentation/Terminology/Thermostats

Best regards,
João

On Tue, Jun 27, 2017 at 11:22 AM, Sergio Manzetti <
sergio.manze...@fjordforsk.no> wrote:

> Hi, I Have run a DNA piece in a box of 7 7 7 , with NaCl ions
> neutralizing, as discussed earlier. The simulation went fine without any
> errors, however it turns out the DNA strands separate. The position
> restraints made by pdb2gmx using the AMBERDB ISTN ff are not working ?
>
> This is the posres file:
> In this topology include file, you will find position restraint
> ; entries for all the heavy atoms in your original pdb file.
> ; This means that all the protons which were added by pdb2gmx are
> ; not restrained.
>
> [ position_restraints ]
> ; atom type fx fy fz
> 1 1 1000 1000 1000
> 3 1 1000 1000 1000
> 6 1 1000 1000 1000
> 8 1 1000 1000 1000
> 9 1 1000 1000 1000
> 11 1 1000 1000 1000
> 12 1 1000 1000 1000
> 14 1 1000 1000 1000
> 15 1 1000 1.
>
>
> and here is the simulation mdp.
>
>
>
>
> itle = DNA in water stabilization
> cpp = /lib/cpp
> include = -I../top
> define =
> integrator = md
> dt = 0.002
> nsteps = 500
> nstxout = 5000
> nstvout = 5000
> nstlog = 5000
> nstenergy = 300
> nstxout-compressed = 300
> compressed-x-grps = DNA SOL NA CL
> energygrps = DNA SOL NA CL
> nstlist = 20
> ns-type = grid
> rlist = 0.8
> coulombtype = PME
> rcoulomb = 0.8
> rvdw = 0.8
> tcoupl = V-Rescale
> tc-grps = SOL DNA NA CL
> tau-t = 0.1 0.1 0.1 0.1
>
>
>
> Note that GMX gromp wanted 4 groups at tc_grps and tau_t, otherwise it
> wouldn't proceed.
>
>
> Thanks!
>
>
> Sergio Manzetti
>
> [ http://www.fjordforsk.no/logo_hr2.jpg ]
>
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
> |   ]
> Midtun
> 6894 Vangsnes
> Norge
> Org.nr. 911 659 654
> Tlf: +47 57695621
> [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ |
> Nanofactory  ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [
> http://www.phap.no/ | FAP ]
>
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[gmx-users] DNA splitting in simulations

[Sergio Manzetti]

Hi, I Have run a DNA piece in a box of 7 7 7 , with NaCl ions neutralizing, as 
discussed earlier. The simulation went fine without any errors, however it 
turns out the DNA strands separate. The position restraints made by pdb2gmx 
using the AMBERDB ISTN ff are not working ? 

This is the posres file: 
In this topology include file, you will find position restraint 
; entries for all the heavy atoms in your original pdb file. 
; This means that all the protons which were added by pdb2gmx are 
; not restrained. 

[ position_restraints ] 
; atom type fx fy fz 
1 1 1000 1000 1000 
3 1 1000 1000 1000 
6 1 1000 1000 1000 
8 1 1000 1000 1000 
9 1 1000 1000 1000 
11 1 1000 1000 1000 
12 1 1000 1000 1000 
14 1 1000 1000 1000 
15 1 1000 1. 


and here is the simulation mdp. 




itle = DNA in water stabilization 
cpp = /lib/cpp 
include = -I../top 
define = 
integrator = md 
dt = 0.002 
nsteps = 500 
nstxout = 5000 
nstvout = 5000 
nstlog = 5000 
nstenergy = 300 
nstxout-compressed = 300 
compressed-x-grps = DNA SOL NA CL 
energygrps = DNA SOL NA CL 
nstlist = 20 
ns-type = grid 
rlist = 0.8 
coulombtype = PME 
rcoulomb = 0.8 
rvdw = 0.8 
tcoupl = V-Rescale 
tc-grps = SOL DNA NA CL 
tau-t = 0.1 0.1 0.1 0.1 



Note that GMX gromp wanted 4 groups at tc_grps and tau_t, otherwise it wouldn't 
proceed. 


Thanks! 


Sergio Manzetti 

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

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

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Re: [gmx-users] Simulations stop running after reaching specific time step

[Vytautas Rakeviius]

Maybe post your mdp file. There are settings about writing out and default 
values if you add nothing too.
 

On Tuesday, June 27, 2017 10:44 AM, Shobha Sharma 
 wrote:
 

 Hello,

I am submitting few simulations, after providing the wall time enough to
finish the jobs. But after reaching a certain time step, in case of all
jobs, the output files are not written beyond that time step.

For example if I check my .log file, using 'tail -f md.log'  I find that it
is not writing anything even though job is running. It utilizes whole wall
time given and ends without writing any further time steps.
In the end it does not even write about any problem faced. Job ends due to
end of wall time.

What might be the reason behind this?

-- 
Thanks and Regards,
Shobha
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Re: [gmx-users] CG MD

[Peter Kroon]

Backwards is one such tool

http://pubs.acs.org/doi/abs/10.1021/ct400617g

http://cgmartini.nl/index.php/tools2/resolution-transformation


Peter


On 26-06-17 18:01, Alex Mathew wrote:
>> though most atomistic properties can be studied by rebuilding the
> atomistic coordinates from the CG. Various methods exist to >do this.
>
> Could you please provide a link to any material or paper for this.


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[gmx-users] Simulations stop running after reaching specific time step

[Shobha Sharma]

Hello,

I am submitting few simulations, after providing the wall time enough to
finish the jobs. But after reaching a certain time step, in case of all
jobs, the output files are not written beyond that time step.

For example if I check my .log file, using 'tail -f md.log'  I find that it
is not writing anything even though job is running. It utilizes whole wall
time given and ends without writing any further time steps.
In the end it does not even write about any problem faced. Job ends due to
end of wall time.

What might be the reason behind this?

-- 
Thanks and Regards,
Shobha
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[gmx-users] Should the peptide be centered initially in the box if we want to calculate its diffusion later?

[Apramita Chand]

Dear All,
Using g_editconf, I am centering the peptide in the box initially. During
equilibration, I'm gradually releasing position restraints. I want the
peptide to be free to move around so that I might calculate its diffusion
constant.
In that case, will centering using -c option restrain its motion ?


yours sincerely
Apramita
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