Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

[Mohammad Hassan Khatami]

Hi Justin, 
I am asked to focus on learning how to change and update the CHARMM36 
parameters, so I could implement the future changes and patches easier. (Thus, 
I am not focused in the Glycan Reader, at the moment.)

Thank you! I think I now have a better understanding of what should I do. For 
each part of my polymer,i.e. the initial, the middle and the final part, I have 
to modify the AGLC molecule to represent each of these parts, seperately.  
So, lets say to introduce the 1->4 linkage, I need to to apply 14ba patch from 
the top_all36_carb.rtf into the merged.rtp file of GROMACS CHARMM36. In this 
case, I need to create a new version of [ AGLC ] molecule (lets call it [ 
AGLC14 ]) in the merged.rtp, with the changes below from the the 
top_all36_carb.rtf, applied to it:
! equatorial-axial 1->4 linkage
PRES 14ba   0.02 ! (i)1->4(i-1) equatorial at C1 and axial at C4
dele atom 1HO4
dele atom 2HO1
dele atom 2O1
ATOM 1C4  CC31610.09 !
ATOM 1O4  OC301-0.36 !
ATOM 2C1  CC31620.29 !
BOND 1O4  2C1
I have to remove the HO4, HO1 and O1 lines and modify the values for the C4, O4 
and C1 atoms. Then, I need to add the bond of 

[ bond ]
…
O4  +C1

Then, I need to apply  the bonds and angles parameters in the the 
top_all36_carb.rtf (below), into the merged.vsd file of the GROMACS CHARMM36.
!IJKL  R(IK)   T(IKJ)PHI   T(JKL)   R(KL)
IC   1C3  1C4  1O4  2C11.5071  110.40  -86.30  121.00   1.3902  ! psi
IC   1C4  1O4  2C1  2O51.4560  121.00 -130.97  108.63   1.4470  ! phi
IC   2O5  1O4 *2C1  2C21.4470  108.63 -122.09  110.89   1.5316
IC   2O5  1O4 *2C1  2H11.4470  108.63  121.92  111.32   1.0837

I have figured out how to implement R(IK), T(IKJ), T(JKL) and R(KL) values into 
the merged.vsd file, except for the PHI values. Where (and/or how) should I put 
it?
Am I on the right track?

Thanks again for your help.
MH


> On May 19, 2017, at 5:36 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 5/19/17 9:57 AM, Mohammad Hassan Khatami wrote:
>> First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf 
>> file I found different linkages for beta-glucose, but non for alpha-glucose.
>> I am trying to make a simple chain with 1->4 linkages like below:
>> 
>> alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose.
>> 
> 
> Linkages are not specific to the sugar; most are totally generic.  A few 
> comments suggest specific usage and may be corner cases, but your patches 
> will be among 14aa, 14ab, 14ba, 14bb.
> 
>> 
>> Then, I might need to branch them with1->6 linkage.
> 
> Also totally possible.
> 
>> I tried Glycan Reader, but itstill crashes.
>> 
> 
> Uploading a correctly named PDB file should work in Glycan Reader or the 
> Quick MD Simulator, but "still crashes" is not diagnostic of anything.  
> Specific help with CHARMM-GUI should be brought to their attention, though.
> 
> -Justin
> 
>> MH
>>> 
 Thanks Justin.
 I have tried the CHARMM-GUI but it crashed. I might need to modify the 
 order of the atoms in my PDB file, which I have created using GLYCAM-Web 
 GUI. I have downloaded the “toppar_c36_feb16” but I did not find a manual 
 on how to apply them (any suggestions?), so it did not go far.
>>> 
>>> What you need to do depends on linkages.  There are patches (PRES in CHARMM 
>>> .rtf files) that tell you how each residue is manipulated in the case of a 
>>> patch; refer to the CHARMM documentation online for specifics.  The file 
>>> you'll need is top_all36_carb.rtf.
>>> 
>>> Otherwise, use the force field files as a template to rename your input 
>>> structure so CHARMM-GUI can process it.  This is probably the much faster 
>>> route.
>>> 
>>> -Justin
>>> 
 I'll play with these two, and I'll be back.
 MH
> On May 18, 2017, at 5:08 PM, Justin Lemkul  wrote:
> 
> 
> 
> On 5/18/17 4:57 PM, Mohammad Hassan Khatami wrote:
>> Hi,
>> 
>> I am trying to run simulations on alpha-D-glucose polymers. I have done 
>> these simulations using AMBER and I am wondering if it is possible to 
>> run them employing CHARMM36 in GROMACS, as well?
>> It seams that CHARMM36 in GROMACS has only implemented monomers of 
>> alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer 
>> to the GROMACS?
>> 
> 
> Sure, you can treat it like any polymer, but you'll have to create the 
> internal monomer residues yourself from the patches in the original 
> CHARMM force field files.
> 
> Or try CHARMM-GUI; it should handle what you need and give you all the 
> necessary GROMACS inputs.
> 
> -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
> 

[gmx-users] Regarding extending simulations with change in .mdp file

[Dilip H N]

Hello,

I have ran a energy minimization, followed by nvt, followed by md run. My
md run mdp (ie., md.mdp) has

dt = 0.002, nsteps = 3000 ; [0.002 * 3000 = 6 ps (60 ns)]
nstxout = 5000 ; save coordinates every 10.0 ps
nstvout = 5000 ; save velocities every 10.0 ps
nstenergy = 5000 ; save energies every 10.0 ps
nstlog= 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps
   ; nstxout-compressed replaces nstxtcout
This simulation i have ran for 60 ns.

Now i need extend the simulation for another 20ns, but with the change in
md.mdp file as:-
dt = 0.001, and nsteps = 2000
nstxout= 1000 ; save coordinates every 1.0 ps
nstvout= 1000 ; save velocities every 1.0 ps
nstenergy = 1000 ; save energies every 1.0 ps
nstlog = 1000 ; update log file every 1.0 ps
nstxout-compressed =1000; save compressed coordinates every 1.0 ps;
   ;nstxout-compressed replaces
nstxtcout
ie., i want the  dt time step of 0.001 and the outputs
(nstxout,nstvout,etc.,) which can save the coordinates for every 1.0ps, for
the 20ns md run.

And then i need to have a  complete run of total 80ns [(60ns of the 1st
mdrun  of dt=0.002*3000) + (20ns of the 2nd mdrun of
dt=0.001*2000)].


How can i do this..??

Thank you.

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] PBC fix for visualization

[Dallas Warren]

I have found the cluster option of -pbc to work well for putting
aggregates back together correctly. Some times you do need an index
file and appropriate groups to assist with it getting it right.

gmx trjconv -pbc cluster
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 16 May 2017 at 07:50, Mohsen Ramezanpour
 wrote:
> Dear Gromacs users,
>
> I have an HII phase made of one inverted cylinder (and waters inside) in a
> triclinic box with 90, 90, 60 angles. After running the simulation, this
> cylinder become bent like a curve. I.e. is not a perfect cylinder anymore.
> As a result, some water molecules and lipids pass the box sides and enter
> from the other side of box because of PBC.
> Now, I want to make the cylinder again but I am not sure how to do so.
>
> The best I could do was to use "-pbc mol  -ur compact" options in trjconv.
> However, here are still some lipids and molecules which are not part of the
> cylinder.
>
> Any idea how could I fix the effect of these PBC in visualization?
>
> Thanks
> Mohsen
>
> --
> *Rewards work better than punishment ...*
> --
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[gmx-users] Radial distribution function

[Sohaib. Mohammed]

Dear all,

I have done a simulation for asphaltene in an organic solvent. The
simulation produces a one cluster contains all the asphaltenes molecules in
the system. I want to calculate the RDF and the cluster profile (i.e.
maximum cluster, average cluster, etc.). Both of them shows strange
results. For example, I simulated N asphaltene molecules, but RDF and
cluster size show both g(r) and MAX Cluster >> N even when I specify the
calculation wrt center of mass of the molecule. The commands I used for the
RDF and max. clust., respectively, as follows:

gmx rdf -f a.xtc -s a.tpr -n index.ndx -o rdf.xvg -selrpos mol_com
gmx clustsize to calculate cluster size

As I think, the maximum cluster should less than or equal to N.

Appreciate any suggestions/comments.

Thank you,
Sohaib
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Re: [gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

Beg your pardon, I have not ignored your comment entirely regarding using
specific residue COM. I just recently succeeded performing md_umbrella
simulation (using protein COM) on few configurations.
.
I have not used specific residues COM so far as because of some confusions
regrading defining it. The residue stretch is not continuous e.g. residue
6-10, 78-80, 56, 63, 35 are to be active site residue. I got no idea how to
define such discrete set of residues using make_ndx command.



On Sun, May 21, 2017 at 8:13 PM, Justin Lemkul  wrote:

>
>
> On 5/21/17 9:47 AM, abhisek Mondal wrote:
>
>> I did try the code successfully on a configuration generated after
>> pulling.
>> The NVT approach with direction-periodic geometry worked nicely for the
>> particular configuration.
>>
>> However, when I tried to reapply the same code (with modified COMs and
>> thus
>> pull_vec) on a different configuration, something awkward happened. The
>> ligand got pulled through protein and got stuck inside it. I have put the
>> trajectory movie alongwith md_umbrella.mdp file here:
>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>>
>> Would you please care to give some advise regarding this odd behavior.
>>
>>
> Likely some elements of your setup are inadequate.  You have a large,
> flexible ligand, so perhaps using its overall COM is inappropriate.  You're
> also using the entire protein COM as the other end of the reaction
> coordinate, and perhaps that's not good enough (I've suggested a number of
> times to be judicious in the choice of residues taken as the group
> corresponding to the protein, but it seems you're simply not doing that so
> I'll stop suggesting it).  Perhaps your pull vector is calculated
> incorrectly.  A lot going on.  Back up and do something simpler, a test
> case that is easy to define so you can get comfortable with setting these
> things up and understanding/diagnosing weird behavior.
>
> -Justin
>
>
> Thank you.
>>
>> On Fri, May 19, 2017 at 5:18 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 5/19/17 5:56 AM, abhisek Mondal wrote:
>>>
>>> On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul  wrote:



> On 5/17/17 8:55 AM, abhisek Mondal wrote:
>
> This time I think I got ligand restrained successfully during the
>
>> umbrella
>> sampling. I have removed the restrain from protein, as per your
>> advice.
>> Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and
>> used
>> pull_rate1=0.0.
>> I have uploaded the trajectory movie (and other mdp files) in the
>> following
>> link:
>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>>
>> However, I'm facing a problem. Due to the withdrawal of the position
>> restrain of protein. The protein and ligand (together) is moving
>> around
>> the
>> box and resulting in "Distance of pull group 1 (10.441990 nm) is
>> larger
>> than 0.49 times the box size (10.646989)" error.
>>
>> As per the video I have uploaded, if I assume this approach worked,
>> then
>> how can I avoid this error ? Is  there any way to make sure the
>> protein-ligand remains in the middle of the box (or nearby). I have
>> taken
>> pretty large box compared to the protein structure from the beginning.
>>
>> Please suggest me a way out.
>>
>>
>> Use a larger box or use direction-periodic geometry.
>>
>
>

  For the sake of computational power I'm leaning towards
 direction-periodic
 geometry. However, from the mailing list entries I found out that
 pressure
 coupling should not be used for this kind of geometry setup.
 NVT coupling with no velocity generation is what I'm opting for. There
 are
 a lot of doubt regarding the md_umbrella.mdp setup using NVT protocol.
 Would you please suggest if the code (
 https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0)
 looks
 sensible ?

 Eagerly waiting for your opinion.


 Try it and see what happens.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> 

Re: [gmx-users] ligand moving out during umbrella sampling

[Justin Lemkul]

On 5/21/17 9:47 AM, abhisek Mondal wrote:

I did try the code successfully on a configuration generated after pulling.
The NVT approach with direction-periodic geometry worked nicely for the
particular configuration.

However, when I tried to reapply the same code (with modified COMs and thus
pull_vec) on a different configuration, something awkward happened. The
ligand got pulled through protein and got stuck inside it. I have put the
trajectory movie alongwith md_umbrella.mdp file here:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

Would you please care to give some advise regarding this odd behavior.



Likely some elements of your setup are inadequate.  You have a large, flexible 
ligand, so perhaps using its overall COM is inappropriate.  You're also using 
the entire protein COM as the other end of the reaction coordinate, and perhaps 
that's not good enough (I've suggested a number of times to be judicious in the 
choice of residues taken as the group corresponding to the protein, but it seems 
you're simply not doing that so I'll stop suggesting it).  Perhaps your pull 
vector is calculated incorrectly.  A lot going on.  Back up and do something 
simpler, a test case that is easy to define so you can get comfortable with 
setting these things up and understanding/diagnosing weird behavior.


-Justin


Thank you.

On Fri, May 19, 2017 at 5:18 PM, Justin Lemkul  wrote:




On 5/19/17 5:56 AM, abhisek Mondal wrote:


On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul  wrote:




On 5/17/17 8:55 AM, abhisek Mondal wrote:

This time I think I got ligand restrained successfully during the

umbrella
sampling. I have removed the restrain from protein, as per your advice.
Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and used
pull_rate1=0.0.
I have uploaded the trajectory movie (and other mdp files) in the
following
link:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

However, I'm facing a problem. Due to the withdrawal of the position
restrain of protein. The protein and ligand (together) is moving around
the
box and resulting in "Distance of pull group 1 (10.441990 nm) is larger
than 0.49 times the box size (10.646989)" error.

As per the video I have uploaded, if I assume this approach worked, then
how can I avoid this error ? Is  there any way to make sure the
protein-ligand remains in the middle of the box (or nearby). I have
taken
pretty large box compared to the protein structure from the beginning.

Please suggest me a way out.


Use a larger box or use direction-periodic geometry.





 For the sake of computational power I'm leaning towards
direction-periodic
geometry. However, from the mailing list entries I found out that pressure
coupling should not be used for this kind of geometry setup.
NVT coupling with no velocity generation is what I'm opting for. There are
a lot of doubt regarding the md_umbrella.mdp setup using NVT protocol.
Would you please suggest if the code (
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0)
looks
sensible ?

Eagerly waiting for your opinion.



Try it and see what happens.

-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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==

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] ligand moving out during umbrella sampling

[abhisek Mondal]

I did try the code successfully on a configuration generated after pulling.
The NVT approach with direction-periodic geometry worked nicely for the
particular configuration.

However, when I tried to reapply the same code (with modified COMs and thus
pull_vec) on a different configuration, something awkward happened. The
ligand got pulled through protein and got stuck inside it. I have put the
trajectory movie alongwith md_umbrella.mdp file here:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

Would you please care to give some advise regarding this odd behavior.

Thank you.

On Fri, May 19, 2017 at 5:18 PM, Justin Lemkul  wrote:

>
>
> On 5/19/17 5:56 AM, abhisek Mondal wrote:
>
>> On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 5/17/17 8:55 AM, abhisek Mondal wrote:
>>>
>>> This time I think I got ligand restrained successfully during the
 umbrella
 sampling. I have removed the restrain from protein, as per your advice.
 Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and used
 pull_rate1=0.0.
 I have uploaded the trajectory movie (and other mdp files) in the
 following
 link:
 https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

 However, I'm facing a problem. Due to the withdrawal of the position
 restrain of protein. The protein and ligand (together) is moving around
 the
 box and resulting in "Distance of pull group 1 (10.441990 nm) is larger
 than 0.49 times the box size (10.646989)" error.

 As per the video I have uploaded, if I assume this approach worked, then
 how can I avoid this error ? Is  there any way to make sure the
 protein-ligand remains in the middle of the box (or nearby). I have
 taken
 pretty large box compared to the protein structure from the beginning.

 Please suggest me a way out.


 Use a larger box or use direction-periodic geometry.
>>>
>>
>>
>>  For the sake of computational power I'm leaning towards
>> direction-periodic
>> geometry. However, from the mailing list entries I found out that pressure
>> coupling should not be used for this kind of geometry setup.
>> NVT coupling with no velocity generation is what I'm opting for. There are
>> a lot of doubt regarding the md_umbrella.mdp setup using NVT protocol.
>> Would you please suggest if the code (
>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0)
>> looks
>> sensible ?
>>
>> Eagerly waiting for your opinion.
>>
>>
> Try it and see what happens.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
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Re: [gmx-users] Nonequilibrium simulations

[jwillcox]

I just reread my e-mail and realized that it was posed as a statement and
not a question.  What I meant was:  When I run non-equilibrium simulations
in the Gromacs code using "acc-groups", is the additional acceleration
considered to contribute to the temperature when velocities are adjusted
or not?

Thank you!

Jon

> Hello,
>
> I am running non-equilibrium simulations using the "acc-groups" command
> and the Nose-Hoover thermostat.  I just wanted to confirm that in Gromacs
> code this additional acceleration is not considered to contribute to the
> temperature when velocities are adjusted.
>
> Thank you!
>
> Jon
>
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Re: [gmx-users] Regarding extending simulations

[Dilip H N]

and which are the commands tht i need to give there.. gmx trjconv or gmx
grommp ..??
Can anybody guide me through this kindly..



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On Sun, May 21, 2017 at 4:40 PM, Dilip H N 
wrote:

> Hello,
> I have ran a energy minimization, followed by nvt, followed by md run. My
> md run mdp (ie., md.mdp) has dt = 0.002, nsteps = 3000 ; [0.002 *
> 3000 = 6 ps (60 ns)]
> nstxout = 5000 ; save coordinates every 10.0 ps
> nstvout = 5000 ; save velocities every 10.0 ps
> nstenergy = 5000 ; save energies every 10.0 ps
> nstlog= 5000 ; update log file every 10.0 ps
> nstxout-compressed = 5000  ; save compressed coordinates every 10.0 ps
> ; nstxout-compressed replaces nstxtcout
> This simulation i have ran for 60 ns.
>
> Now i need extend the simulation for another 20ns, but with the change in
> md.mdp file as:-
> dt = 0.001, and nsteps = 
> nstxout= 1000 ; save coordinates every 1.0 ps
> nstvout= 1000 ; save velocities every 1.0 ps
> nstenergy = 1000 ; save energies every 1.0 ps
> nstlog = 1000 ; update log file every 1.0 ps
> nstxout-compressed =1000; save compressed coordinates every 1.0 ps
> ie., i want the  dt time step of 0.001 and the outputs
> (nstxout,nstvout,etc.,) which can save the coordinates for every 1.0ps, for
> the 20ns run.
> I want to run the simulation for extra another 20ns by changing the md.mdp
> for 0.001 dt and saving the coordinates for every 1.0 ps.
> And thn i will have a complete run of total 80ns [(60ns of the 1st mdrun
>  of dt=0.002*3000) + (next 2nd mdrun of dt=0.001*)].
>
> So wht are the changes tht i need to do in the mdp file.. if i change dt
> to 0.001and wht should be the nsteps() value..and changing the output
> steps tht i want to save, such tht i get a run for 20ns , and which will
> give me a total of 80ns..
>
>
> Thank you
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>    Sent with Mailtrack
> 
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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[gmx-users] Regarding extending simulations

[Dilip H N]

Hello,
I have ran a energy minimization, followed by nvt, followed by md run. My
md run mdp (ie., md.mdp) has dt = 0.002, nsteps = 3000 ; [0.002 *
3000 = 6 ps (60 ns)]
nstxout = 5000 ; save coordinates every 10.0 ps
nstvout = 5000 ; save velocities every 10.0 ps
nstenergy = 5000 ; save energies every 10.0 ps
nstlog= 5000 ; update log file every 10.0 ps
nstxout-compressed = 5000  ; save compressed coordinates every 10.0 ps
; nstxout-compressed replaces nstxtcout
This simulation i have ran for 60 ns.

Now i need extend the simulation for another 20ns, but with the change in
md.mdp file as:-
dt = 0.001, and nsteps = 
nstxout= 1000 ; save coordinates every 1.0 ps
nstvout= 1000 ; save velocities every 1.0 ps
nstenergy = 1000 ; save energies every 1.0 ps
nstlog = 1000 ; update log file every 1.0 ps
nstxout-compressed =1000; save compressed coordinates every 1.0 ps
ie., i want the  dt time step of 0.001 and the outputs
(nstxout,nstvout,etc.,) which can save the coordinates for every 1.0ps, for
the 20ns run.
I want to run the simulation for extra another 20ns by changing the md.mdp
for 0.001 dt and saving the coordinates for every 1.0 ps.
And thn i will have a complete run of total 80ns [(60ns of the 1st mdrun
 of dt=0.002*3000) + (next 2nd mdrun of dt=0.001*)].

So wht are the changes tht i need to do in the mdp file.. if i change dt to
0.001and wht should be the nsteps() value..and changing the output
steps tht i want to save, such tht i get a run for 20ns , and which will
give me a total of 80ns..


Thank you
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] pdb2gmx do not work for unstable conformations

[ZHANG Cheng]

Dear Mark Abraham,
Thank you so much for debugging it for me. The strange word could only be seen 
under Unix environment. After using dos2unix, the problem finally solves! 


I totally forgot to always use dos2unix. Thanks a lot for reminding me again!


Yours sincerely
Cheng




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Sat, May 20, 2017 09:32 PM
To:  "gromacs.org_gmx-users"; 
Cc:  "ZHANG Cheng"<272699...@qq.com>; 
Subject:  pdb2gmx do not work for unstable conformations



Dear Gromacs,I have a protein PDB structure as well as its mutants PDB, 
predicted by Rosetta with different ddG. After running pdb2gmx, I found that 
the structures with lower ddG (more stable) all perform okay; while structures 
with higher ddG (less stable) got fatal error:


Fatal error:
Residue 1 named ASP of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.


For example, I got fatal error for:
gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh 
-merge interactive

But it works fine for: 
gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water spce -inter -ignh -merge 
interactive
 (just change to another stable mutant, but the first residue ASP is the same)


But I could not figure out the exact reasons for the fatal error.


I have attached two stable PDB and two unstable PDB:
https://1drv.ms/f/s!AjIs-W_id1LzobIlN0o5fxW49-Fmmg

Could you please help me to find out the reasons?


Thank you very much.


Yours sincerely
Cheng



All the screen output is below, quite long:
--
lanselibai@ubuntu:~/Cheng/gromacs/20170517_370K_paper1_mutants/HC_V215W$ gmx 
pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh 
-merge interactive
GROMACS:gmx pdb2gmx, VERSION 5.0.4

GROMACS is written by:
Emile Apol Rossen Apostolov   Herman J.C. Berendsen Par Bjelkmar   
Aldert van Buuren  Rudi van DrunenAnton Feenstra Sebastian Fritsch  
Gerrit GroenhofChristoph Junghans Peter Kasson   Carsten Kutzner
Per LarssonJustin A. Lemkul   Magnus LundborgPieter Meulenhoff  
Erik Marklund  Teemu Murtola  Szilard Pall   Sander Pronk   
Roland Schulz  Alexey ShvetsovMichael Shirts Alfons Sijbers 
Peter Tieleman Christian Wennberg Maarten Wolf   
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx pdb2gmx, VERSION 5.0.4
Executable:   /usr/local/gromacs/bin/gmx
Library dir:  /usr/local/gromacs/share/gromacs/top
Command line:
  gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter 
-ignh -merge interactive


Select the Force Field:
>From '/usr/local/gromacs/share/gromacs/top':
 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
1999-2012, 2003)
 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
461-469, 1996)
 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
1049-1074, 2000)
 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
2006)
 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
78, 1950-58, 2010)
 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
 9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
15

Using the Oplsaa force field in directory oplsaa.ff

Opening force field file 
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b
Reading HC_V215W.pdb...
Read 3342 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
Merge chain ending with residue CYS214 (chain id 'L', atom 3258 SG) and chain 
starting with
residue GLU215 (chain id 'H', atom