Re: [gmx-users] Unrealistic behaviour of water on graphene [NVT]

[Tsjerk Wassenaar]

Hi Kester,

Do you have experimental data on the behaviour of 2000 or 6000 or 1
water molecules on a sheet of graphene? Do you _know_ it's wrong behaviour?
If yes, then, given that the water forms a droplet in vacuum, even if above
the graphene sheet, you know the water behaviour itself is sort of correct.
I would be most suspicious of the water-graphene interactions. Where did
those parameters come from? Do they account for increased electron density
above the plane because of all the pi-orbitals?

Cheers,

Tsjerk


On Tue, Sep 2, 2014 at 8:24 AM, Kester Wong kester2...@ibs.re.kr wrote:

 Dear gmx-users,


 I am modelling a water droplet using a water box model, and have
 encountered unrealistic behaviour of equilibrating water on graphene, using
 GRAPPA force field in GROMACS 5.0.

 The box size is about 30x30x15 nm. Structure-wise, the water models (2000,
 6000, and 10,000 water molecules) appear to be spreading like a flat
 layer of solution, rather than a droplet.

 Additionally, for the 10,000 molecules on graphene, water droplet was
 formed in vacuo above the surface.


 I have posted some questions on GROMACS user list, however, I have yet to
 receive any feedback.

 Could anyone please look at my .mdp parameter and the .xtc trajectory
 files? I do not know what caused the spreading of water on graphene.


 There are two parameter settings that I have used, they are labeled as
 lincs-order=4 (larger temperature constant and time-step), and
 lincs-order=8 (smaller temperature constant and time-step).
 The starting configuration (pdb), trajectories (xtc), and parameter (mdp)
 files are uploaded in my Google Drive:
 ​


 https://drive.google.com/folderview?id=0B7ym8d6G9-e2Tlh4VGNSaDhCbmcusp=sharing


 https://drive.google.com/folderview?id=0B7ym8d6G9-e2Rl9WaXNrUlVRa28usp=sharing


 https://drive.google.com/folderview?id=0B7ym8d6G9-e2bnFzbWN3VHVqbE0usp=sharing


 Please let me know if you need more information/files on the GRAPPA-based
 calculations.

 Any help will be tremendously appreciated.



 Regards,

 Kester


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Re: [gmx-users] correction of g_principal bug

[nicola staffolani]

Thank you!


2014-09-01 19:24 GMT+02:00 Justin Lemkul jalem...@vt.edu:



 On 9/1/14, 10:45 AM, nicola staffolani wrote:

 which substantially means this
 http://www.gromacs.org/Documentation/Installation_
 Instructions#quick-and-dirty-installation,
 right?


 Install it however you normally do.

 -Justin



 2014-09-01 15:42 GMT+02:00 Justin Lemkul jalem...@vt.edu:



 On 9/1/14, 9:09 AM, nicola staffolani wrote:

  ​Dear GROMACS community,

 regarding this reported bug
 http://permalink.gmane.org/gmane.science.biology.gromacs.user/66719
 of

 g_principal, I have edited gmx_principal.c in my
 ~/GROMACS/gromacs-4.5.5/src/tools folder as described, I have then left
 gromacs run, but in my /usr/bin folder I see that g_principal has been
 modified the last time somewhen in 2011; from this I draw the conclusion
 that the bug is still there in my gromacs program; could you kindly tell
 me
 what to do?

 I guess something resembling a compilation and/or a linking is
 missing...


  If you change the code, you have to recompile and reinstall for
 anything
 to take effect.

 -Justin

 --
 ==

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

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 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 601
 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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-- 
Nicola Staffolani PhD
Biophysics  Nanoscience Centre CNISM http://www.unitus.it/biophysics
Università della Tuscia
Largo dell'Università s.n.c., I-01100 Viterbo
email: n.staffol...@unitus.it
tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36
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Re: [gmx-users] Unrealistic behaviour of water on graphene [NVT]

[Kester Wong]

Hi Tsjerk, Do you have experimental data on the behaviour of 2000 or 6000 or 1 water molecules on a sheet of graphene? There are experimental and theoretical data that describe the contact angle of water on graphene. Current experimental data of water droplets on a sheet of graphene can be found in the work byRafiee et al., Nature Materials Vol. 11 217-222 (2012), Li et al., Nature Materials Vol. 12 925-931(2013), and Zhou et al., Phys. Rev. B 85, 035406 (2012).Theoretical calculations of the 2000, 6000, and 10,000 molecules have also been reported by Shih et al., Nature Materials (Commentary) Vol. 12 866-869 (2013),Shih et al., PRL 109, 176101 (2012),and Taherian et al., Langmuir 29, 1457-1465 (2013), just to name a few. Do you _know_ it's wrong behaviour?Since I am new to gromacs calculations, I am afraid I do not know what went wrong with the calculation. Either the effect of polarisation makes the surface superhydrophilic, or the neighbouring interaction prevents water from forming a droplet.Water should, however, form a droplet on the surface. If yes, then, given that the water forms a droplet in vacuum, even if above
 the graphene sheet, you know the water behaviour itself is sort of correct.
 I would be most suspicious of the water-graphene interactions. Where did those parameters come from?GRAPPA force field (Hughes et al., Nanoscale 6, 5438-5448 (2014)) was developed based on CHARMM FF, where the FF parameters were obtained through first deriving a set of C-C parameters, following by the parameters of different oxygen-containing species.Another similar polarisable FF was also recently developed based on OPLS/AA by Schyman and Jorgensen, J. Phys. Chem. Lett. 4, 468-474 (2013). Do they account for increased electron density
 above the plane because of all the pi-orbitals?I am not absolutely certain that the pi-orbitals were accounted for, however, the authors have described that GRAPPA can capture the overlap of pi-electron cloud between residue and graphene surface.Regards,Kester
Do you have experimental data on the behaviour of 2000 or 6000 or 1
water molecules on a sheet of graphene? Do you _know_ it's wrong behaviour?
If yes, then, given that the water forms a droplet in vacuum, even if above
the graphene sheet, you know the water behaviour itself is sort of correct.
I would be most suspicious of the water-graphene interactions. Where did
those parameters come from? Do they account for increased electron density
above the plane because of all the pi-orbitals?

Cheers,

Tsjerk


On Tue, Sep 2, 2014 at 8:24 AM, Kester Wong  wrote:

 Dear gmx-users,


 I am modelling a water droplet using a water box model, and have
 encountered unrealistic behaviour of equilibrating water on graphene, using
 GRAPPA force field in GROMACS 5.0.

 The box size is about 30x30x15 nm. Structure-wise, the water models (2000,
 6000, and 10,000 water molecules) appear to be spreading like a flat
 layer of solution, rather than a droplet.

 Additionally, for the 10,000 molecules on graphene, water droplet was
 formed in vacuo above the surface.


 I have posted some questions on GROMACS user list, however, I have yet to
 receive any feedback.

 Could anyone please look at my .mdp parameter and the .xtc trajectory
 files? I do not know what caused the spreading of water on graphene.


 There are two parameter settings that I have used, they are labeled as
 lincs-order=4 (larger temperature constant and time-step), and
 lincs-order=8 (smaller temperature constant and time-step).
 The starting configuration (pdb), trajectories (xtc), and parameter (mdp)
 files are uploaded in my Google Drive:
 ​


 https://drive.google.com/folderview?id=0B7ym8d6G9-e2Tlh4VGNSaDhCbmcusp=sharing


 https://drive.google.com/folderview?id=0B7ym8d6G9-e2Rl9WaXNrUlVRa28usp=sharing


 https://drive.google.com/folderview?id=0B7ym8d6G9-e2bnFzbWN3VHVqbE0usp=sharing


 Please let me know if you need more information/files on the GRAPPA-based
 calculations.

 Any help will be tremendously appreciated.



 Regards,

 Kester


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Tsjerk A. Wassenaar, Ph.D.
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[gmx-users] changing the viscosity of water in a simulation

[soumadwip ghosh]

Hello,

  I am a newbie to MD simulation. We are working in the direction of
finding the molecular origin of internal friction of protein folding. For
this we have to run folding simulations at different solvent viscosity and
plot protein reconfiguration time against solvent viscosity. Currently, we
have been using TIP3P water molecules for simulations run on GROMACS 4.5.6.
I wwill be highly grateful if someone tells me how to change the viscosity
of water.

Best,
Soumadwip.
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[gmx-users] template.c is needed for Gromacs 5.0

[Bert]

Hi all,

I used to write my own analysis code using C-based template.c. However,
only C++-based template.cpp is provided in the recent 5.0 package. Like
many people, I know little about the C++ code, I wonder if there is an
alternative C-based template available for us. Thanks in advance.

Best regards,
Bert
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[gmx-users] tab completion gmx

[Viveca Lindahl]

Hi all,

Should I expect the tab completion of gmx to work (e.g. as with git)? Or is
the idea to create aliases like g_energy='gmx energy' for everything that I
use?

Viveca
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Re: [gmx-users] GPU and MPI

[Szilárd Páll]

You may want to try other settings between 4x6 and 24x1 too, e.g. 12x2
or 6x4 - especially if you have a dual-socket 6-core machine with
HyperThreading. In my experience, using as many ranks as hardware
threads with HT in GPU runs results in big slowdown compared to either
not using HT (i.e. 12x1) or using 2 threads/rank (12x2).

Cheers,
--
Szilárd


On Mon, Sep 1, 2014 at 5:13 PM, Carsten Kutzner ckut...@gwdg.de wrote:

 On 01 Sep 2014, at 15:58, Da-Wei Li lida...@gmail.com wrote:

 No. With GPU, both domain and PME domain are decomposited by 4X1X1, because
 I use 4 MPI ranks, in line with 4 GPUs. W/o GPU, domain decomposition is
 20X1X1 and PME is 4X1X1.
 So the difference in performance could be due to the different DD and
 PME/PP settings. I would try to use exactly the same settings with and
 without GPU. With GPUs, you then would need to specify something like

 mpirun -n 24 mdrun -dd 20 1 1 -npme 4 -gpu_id 01

 So you get 10 DD plus 2 PME ranks per node and map the first 5 DD ranks
 to GPU id 0, and the last 5 DD ranks to GPU id 1.

 Carsten



 dawei


 On Mon, Sep 1, 2014 at 8:39 AM, Carsten Kutzner ckut...@gwdg.de wrote:

 Hi Dawei,

 on two nodes, regarding the cases with and without GPUs,
 do you use the same domain decomposition in both cases?

 Carsten


 On 01 Sep 2014, at 14:30, Da-Wei Li lida...@gmail.com wrote:

 I have added  -resethway but still the same result. Use two GPU and 12
 cores distributed in 2 nodes will result 33 ns/day, that is, it is about
 3
 time slower than MD run on one node (2GPU+12core).

 I have no idea what is wrong.


 dawei


 On Mon, Sep 1, 2014 at 5:34 AM, Carsten Kutzner ckut...@gwdg.de wrote:

 Hi,

 take a look at mdrun’s hidden but sometimes useful options:

 mdrun -h -hiddden

 Carsten


 On 01 Sep 2014, at 11:07, Oliver Schillinger 
 o.schillin...@fz-juelich.de
 wrote:

 Hi,
 I did not know about the -resethway command line switch to mdrun.
 Why is it nowhere documented?
 Or am I blind/stupid?
 Cheers,
 Oliver

 On 08/29/2014 05:15 PM, Carsten Kutzner wrote:
 Hi Dawei,

 On 29 Aug 2014, at 16:52, Da-Wei Li lida...@gmail.com wrote:

 Dear Carsten

 Thanks for the clarification. Here it is my benchmark for a small
 protein
 system (18k atoms).

 (1) 1 node (12 cores/node, no GPU):   50 ns/day
 (2) 2 nodes (12 cores/node, no GPU): 80 ns/day
 (3) 1 node (12 cores/node, 2 K40 GPUs/node): 100 ns/day
 (4) 2 nodes (12 cores/node, 2 K40 GPUs/node): 40 ns/day


 I send out this question because the benchmark 4 above is very
 suspicious.
 Indeed, if you get 80 ns/day without GPUs, then it should not be less
 with GPUs. For how many time steps do you run each of the
 benchmarks? Do you use the -resethway command line switch to mdrun
 to disregard the first half of the run (where initialization and
 balancing is done, you don’t want to count that in a benchmark)?

 Carsten

 But I agree size of my system may play a role.

 best,

 dawei


 On Fri, Aug 29, 2014 at 10:36 AM, Carsten Kutzner ckut...@gwdg.de
 wrote:

 Hi Dawei,

 the mapping of GPUs to PP ranks is printed for the Master node only,
 but if this node reports two GPUs, then all other PP ranks will also
 use two GPUs (or an error is reported).

 The scaling will depend also on your system size, if this is too
 small,
 then you might be better off by using a single node.

 Carsten


 On 29 Aug 2014, at 16:24, Da-Wei Li lida...@gmail.com wrote:

 Dear users,

 I recently try to run Gromacs on two nodes, each of them has 12
 cores
 and 2
 GPUs. The nodes are connected with infiniband and scaling is pretty
 good
 when no GPU is evolved.

 My command is like this:

 mpiexec  -npernode 2 -np 4 mdrun_mpi -ntomp 6


 However, it looks like Gromacs only detected 2 GPUs on node 0, then
 skip
 node 1. Part of the output looks like:


 

 Using 4 MPI processes

 Using 6 OpenMP threads per MPI process

 2 GPUs detected on host n0316.ten:

 #0: NVIDIA Tesla M2070, compute cap.: 2.0, ECC: yes, stat:
 compatible

 #1: NVIDIA Tesla M2070, compute cap.: 2.0, ECC: yes, stat:
 compatible

 2 GPUs user-selected for this run.

 Mapping of GPUs to the 2 PP ranks in this node: #0, #1

 


 The performance is about only 40% of the run, where I use only 1
 node (12
 cores+2GPUs).


 Does I miss something?


 thanks.


 dawei
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[gmx-users] Energy minimization problem after editconf step

[neha bharti]

Hello All

I am trying to perform MD for protein ligand complex in popc lipid with
Charmm36 force field. I follow Justin A. Lemkul tutorial of membrane
protein simulation.

I have successfully perform till InflateGRO followed by energy minimization
step.

perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat

 grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr

mdrun -v -deffnm em

till 24 iteration then I reached area per lipid 0.70 nm^2

when I visualize the molecule then the box size small in Z axis so in
editconf step I increase the box size and then add solvent and ion . when I
increase the box size with editconf then there is atomic clashes occur.and
giving following error:

Steepest Descents converged to machine precision in 18 steps,
 but did not reach the requested Fmax  1000.
 Potential Energy  =  6.1499341e+20
 Maximum force =inf on atom 3300
Norm of force =  5.4206209e+1


 When I skip this step (editconf) then the minimization is normal.
But I need to increase the box size.
How to increase the box size?

Please help

With Regards
Neha bharty
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[gmx-users] Reminder about Gromacs user survey

[Michael Shirts]

Dear Gromacs users/developers,

I'd like to remind you about the currently running Gromacs feature and user
survey Mark Abraham emailed out last week. The survey can be found at:

https://www.surveymonkey.com/s/BD63LRP

We've had a lot of great feedback so far, but would love to hear your
thoughts and opinions as well!

Those filling out the survey will be eligible for the previously detailed
random drawing of two $50 Amazon gift certificates.  Due to Labor Day
weekend in the US cutting the beginning of this week short, we will extend
the original eligibility deadline from 11:59 p.m. GMT tonight (September
2nd) until 11:59 p.m. Pacific Daylight Time tomorrow, Wednesday, September
3rd.

Best,

Michael Shirts
Associate Professor
Department of Chemical Engineering
University of Virginia
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Re: [gmx-users] tab completion gmx

[Mark Abraham]

Hi,

Yes, with GMXRC sourced, under bash you should see completion work in the
same kind of way that git does.

Mark


On Tue, Sep 2, 2014 at 11:31 AM, Viveca Lindahl vive...@kth.se wrote:

 Hi all,

 Should I expect the tab completion of gmx to work (e.g. as with git)? Or is
 the idea to create aliases like g_energy='gmx energy' for everything that I
 use?

 Viveca
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Re: [gmx-users] Energy minimization problem after editconf step

[neha bharti]

Thanks for your reply Justin

The error is now solve but I don't know this is a right way or not.


The step which I perform previously in which I am facing error:

Packing :

1) perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
area_shrink1.dat

2) grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr

3) mdrun -v -deffnm em

I did this till 24 iteration then I reached area per lipid 0.70 nm^2



4) Adding Solvent:

a) editconf -f system_shrink.gro -o POPC_box.gro -box 8.68740 8.41864
12.70145

b) genbox -cp  POPC_box.gro -cs spc216.gro -o  POPC_sol.gro



5) Adding Ions

a) grompp -f ion.mdp -c POPC_sol.gro -p topol.top -o ion.tpr

b) genion -s ion.tpr -o POPC_sol_ions.gro -p topol.top -pname NA -np 1
-nname CL

Select 16 to add 1 possitive ion to sol



6) Energy Minimization

Next, energy minimize the entire system now, using the following commands:

a) grompp -f em.mdp -c POPC_sol_ions.gro -p topol.top -o em.tpr

b) mdrun -v -deffnm em



In energy minimization step
The following error occur

Steepest Descents converged to machine precision in 18 steps,
 but did not reach the requested Fmax  1000.
 Potential Energy  =  6.1499341e+20
 Maximum force =inf on atom 3300
Norm of force =  5.4206209e+1

But if I skip the editconf step 4(a) the the energy minimization is normal.
But i need to increase the box size because my protein is out of the box.


So I did some changes before the packing which gives the correct result.
The steps are as follows:


Before energy minimization of POPC.gro I remove the water (SOL molecule
manually) then increase the box size by

1) editconf -f POPC.gro -o popc_new.gro -box 8.68740 8.41864 15 : With the
help of this command I increase the box size of popc.gro which I have
downloaded. ( Peter C. Lai POPC lipid http://cesium.hyperfine.info/~peter
/gromacs/popc36/ )


2) genbox -cp  POPC_new.gro -cs spc216.gro -o  POPC_new_sol.gro : Add
solvent


3) Energy minimization:
a) grompp -f em.mdp -c POPC_new_sol.gro -p topol_popc.top -o em.tpr
b) mdrun -v -deffnm em

4) trjconv to remove periodicity:

trjconv -s em.tpr -f em.gro -o popc_whole.gro -pbc mol -ur compact

select 0 for system

orient the KALP peptide within this same coordinate frame as popc_whole.gro

editconf -f conf.gro -o conf_newbox.gro -c -box 8.68740 8.41864 12.70145

Rest of the step is same as above after packing I took system_shrink24.gro
without using editconf because I already arrange the size of the box like

 Adding Solvent:

a) genbox -cp  system_shrink24.gro -cs spc216.gro -o  POPC_sol.gro



 Adding Ions

a) grompp -f ion.mdp -c POPC_sol.gro -p topol.top -o ion.tpr

b) genion -s ion.tpr -o POPC_sol_ions.gro -p topol.top -pname NA -np 1
-nname CL

Select 16 to add 1 possitive ion to sol



6) Energy Minimization

Next, energy minimize the entire system now, using the following commands:

a) grompp -f em.mdp -c POPC_sol_ions.gro -p topol.top -o em.tpr

b) mdrun -v -deffnm em


When I perform by above method my energy minimization occur.
Is this the right way??

Thanks

With Regards

Neha bharty




  Hello All

  I am trying to perform MD for protein ligand complex in popc lipid with
  Charmm36 force field. I follow Justin A. Lemkul tutorial of membrane
  protein simulation.

  I have successfully perform till InflateGRO followed by energy
minimization
  step.

  perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
area_shrink1.dat

grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr

  mdrun -v -deffnm em

  till 24 iteration then I reached area per lipid 0.70 nm^2

  when I visualize the molecule then the box size small in Z axis so in
  editconf step I increase the box size and then add solvent and ion .
when I
  increase the box size with editconf then there is atomic clashes
occur.and
  giving following error:

  Steepest Descents converged to machine precision in 18 steps,
   but did not reach the requested Fmax  1000.
   Potential Energy  =  6.1499341e+20
   Maximum force =inf on atom 3300
 Norm of force =  5.4206209e+1


   When I skip this step (editconf) then the minimization is normal.
 But I need to increase the box size.
 How to increase the box size?


You need to provide the exact commands that you used when manipulating the
box,
otherwise it's pure guesswork.
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[gmx-users] How to mearg Ligand protein and Lipid

[neha bharti]

Hello All

I am trying to perform MD for protein ligand protein complex in popc lipid
with
charmm36 force field and also follow Justin A. Lemkul tutorial.

I also wanted to ask that while create special index groups consisting of
solvent + ions and protein + lipids using make_ndx if i am having a system
with ligand molecule also then should I add it with protein lipid complex
or add it separately with protein like

16 | 14 to merge the SOL and CL groups

1 | 13 | to merge Protein and POPC groups

and
1 | 12 to merge Protein and LIGAND groups

or I can add them like 1 | 12 | 13 to merge Protein and LIGAND and POPC
groups

With Regards
Neha bharty
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Re: [gmx-users] changing the viscosity of water in a simulation

[Dr. Vitaly Chaban]

On Tue, Sep 2, 2014 at 10:59 AM, soumadwip ghosh
soumadwipgh...@gmail.com wrote:
 Hello,

   I am a newbie to MD simulation. We are working in the direction of
 finding the molecular origin of internal friction of protein folding. For
 this we have to run folding simulations at different solvent viscosity and
 plot protein reconfiguration time against solvent viscosity. Currently, we
 have been using TIP3P water molecules for simulations run on GROMACS 4.5.6.
 I wwill be highly grateful if someone tells me how to change the viscosity
 of water.


To change water viscosity, you must be assigned as God.

Pick up another FFM.


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН



 Best,
 Soumadwip.
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Re: [gmx-users] Energy minimization problem after editconf step

[Justin Lemkul]

On 9/2/14, 10:49 AM, neha bharti wrote:

Thanks for your reply Justin

The error is now solve but I don't know this is a right way or not.


The step which I perform previously in which I am facing error:

Packing :

1) perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
area_shrink1.dat

2) grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr

3) mdrun -v -deffnm em

I did this till 24 iteration then I reached area per lipid 0.70 nm^2



4) Adding Solvent:

a) editconf -f system_shrink.gro -o POPC_box.gro -box 8.68740 8.41864
12.70145

b) genbox -cp  POPC_box.gro -cs spc216.gro -o  POPC_sol.gro



5) Adding Ions

a) grompp -f ion.mdp -c POPC_sol.gro -p topol.top -o ion.tpr

b) genion -s ion.tpr -o POPC_sol_ions.gro -p topol.top -pname NA -np 1
-nname CL

Select 16 to add 1 possitive ion to sol



6) Energy Minimization

Next, energy minimize the entire system now, using the following commands:

a) grompp -f em.mdp -c POPC_sol_ions.gro -p topol.top -o em.tpr

b) mdrun -v -deffnm em



In energy minimization step
The following error occur

Steepest Descents converged to machine precision in 18 steps,
  but did not reach the requested Fmax  1000.
  Potential Energy  =  6.1499341e+20
  Maximum force =inf on atom 3300
Norm of force =  5.4206209e+1

But if I skip the editconf step 4(a) the the energy minimization is normal.
But i need to increase the box size because my protein is out of the box.


So I did some changes before the packing which gives the correct result.
The steps are as follows:


Before energy minimization of POPC.gro I remove the water (SOL molecule
manually) then increase the box size by

1) editconf -f POPC.gro -o popc_new.gro -box 8.68740 8.41864 15 : With the
help of this command I increase the box size of popc.gro which I have
downloaded. ( Peter C. Lai POPC lipid http://cesium.hyperfine.info/~peter
/gromacs/popc36/ )


2) genbox -cp  POPC_new.gro -cs spc216.gro -o  POPC_new_sol.gro : Add
solvent


3) Energy minimization:
a) grompp -f em.mdp -c POPC_new_sol.gro -p topol_popc.top -o em.tpr
b) mdrun -v -deffnm em

4) trjconv to remove periodicity:

trjconv -s em.tpr -f em.gro -o popc_whole.gro -pbc mol -ur compact

select 0 for system

orient the KALP peptide within this same coordinate frame as popc_whole.gro

editconf -f conf.gro -o conf_newbox.gro -c -box 8.68740 8.41864 12.70145

Rest of the step is same as above after packing I took system_shrink24.gro
without using editconf because I already arrange the size of the box like

  Adding Solvent:

a) genbox -cp  system_shrink24.gro -cs spc216.gro -o  POPC_sol.gro



  Adding Ions

a) grompp -f ion.mdp -c POPC_sol.gro -p topol.top -o ion.tpr

b) genion -s ion.tpr -o POPC_sol_ions.gro -p topol.top -pname NA -np 1
-nname CL

Select 16 to add 1 possitive ion to sol



6) Energy Minimization

Next, energy minimize the entire system now, using the following commands:

a) grompp -f em.mdp -c POPC_sol_ions.gro -p topol.top -o em.tpr

b) mdrun -v -deffnm em


When I perform by above method my energy minimization occur.
Is this the right way??



If it works, you can't argue with results.  I don't know why the first method 
didn't work, but it appears you've found a solution.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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 mearg Ligand protein and Lipid

[Justin Lemkul]

On 9/2/14, 10:52 AM, neha bharti wrote:

Hello All

I am trying to perform MD for protein ligand protein complex in popc lipid
with
charmm36 force field and also follow Justin A. Lemkul tutorial.

I also wanted to ask that while create special index groups consisting of
solvent + ions and protein + lipids using make_ndx if i am having a system
with ligand molecule also then should I add it with protein lipid complex
or add it separately with protein like

16 | 14 to merge the SOL and CL groups

1 | 13 | to merge Protein and POPC groups

and
1 | 12 to merge Protein and LIGAND groups

or I can add them like 1 | 12 | 13 to merge Protein and LIGAND and POPC
groups


Yes, this is the proper way to merge three groups.

I would likely create 3 tc-grps: protein+ligand, lipids, and solvent+ions.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] Creating an ITP file for charmm27

[Kester Wong]

Dear gmx-users,I have manually created a graphene.itp file for charmm27 forcefield calculations, with the intention to model the contact angle of water.The atomic mass and charge values were obtained from the forcefield ffnonbonded.itp.Could anyone please advise if my file is correct?[ moleculetype ];name nrexclGRA  3[ atoms ]; id  at type  resnum resname atname cg no charge mass 1  C 1 GRA  C   1 0.51  12.011 2  C 1 GRA  C   2 0.51  12.011 3  C 1 GRA  C   3 0.51  12.011 4  C 1 GRA  C   4 0.51  12.011 5  C 1 GRA  C   5 0.51  12.011 6  C 1 GRA  C   6 0.51  12.011 7  C 1 GRA  C   7 0.51  12.011 8  C 1 GRA  C   8 0.51  12.011 9  C 1 GRA  C   9 0.51  12.011 10  C 1 GRA  C  10 0.51  12.011 11  C 1 GRA  C  11 0.51  12.011 12  C 1 GRA  C  12 0.51  12.011 13  C 1 GRA  C  13 0.51  12.011 14  C 1 GRA  C  14 0.51  12.011 15  C 1 GRA  C  15 0.51  12.011 16  C 1 GRA  C  16 0.51  12.011 17  C 1 GRA  C  17 0.51  12.011 18  C 1 GRA  C  18 0.51  12.011 19  C 1 GRA  C  19 0.51  12.011 20  C 1 GRA  C  20 0.51  12.011 21  C 1 GRA  C  21 0.51  12.011 22  C 1 GRA  C  22 0.51  12.011 23  C 1 GRA  C  23 0.51  12.011 24  C 1 GRA  C  24 0.51  12.011 25  C 1 GRA  C  25 0.51  12.011 26  C 1 GRA  C  26 0.51  12.011 27  C 1 GRA  C  27 0.51  12.011 28  C 1 GRA  C  28 0.51  12.011 29  C 1 GRA  C  29 0.51  12.011 30  C 1 GRA  C  30 0.51  12.011 31  C 1 GRA  C  31 0.51  12.011 32  C 1 GRA  C  32 0.51  12.011 33  C 1 GRA  C  33 0.51  12.011 34  C 1 GRA  C  34 0.51  12.011 35  C 1 GRA  C  35 0.51  12.011 36  C 1 GRA  C  36 0.51  12.011 37  C 1 GRA  C  37 0.51  12.011 38  C 1 GRA  C  38 0.51  12.011 39  C 1 GRA  C  39 0.51  12.011 40  C 1 GRA  C  40 0.51  12.011 41  C 1 GRA  C  41 0.51  12.011 42  C 1 GRA  C  42 0.51  12.011 43  C 1 GRA  C  43 0.51  12.011 44  C 1 GRA  C  44 0.51  12.011 45  C 1 GRA  C  45 0.51  12.011 46  C 1 GRA  C  46 0.51  12.011 47  C 1 GRA  C  47 0.51  12.011 48  C 1 GRA  C  48 0.51  12.011 49  C 1 GRA  C  49 0.51  12.011 50  C 1 GRA  C  50 0.51  12.011 51  C 1 GRA  C  51 0.51  12.011 52  C 1 GRA  C  52 0.51  12.011 53  C 1 GRA  C  53 0.51  12.011 54  C 1 GRA  C  54 0.51  12.011 55  C 1 GRA  C  55 0.51  12.011 56  C 1 GRA  C  56 0.51  12.011 57  C 1 GRA  C  57 0.51  12.011 58  C 1 GRA  C  58 0.51  12.011 59  C 1 GRA  C  59 0.51  12.011 60  C 1 GRA  C  60 0.51  12.011In the tutorial by Andrea Minoia (http://chembytes.wikidot.com/grocnt), all the charges of graphene were set to zero, but I have decided to keep the graphene surface charges.Has anyone looked at the difference between the water/graphene interaction, having a charged graphene .itp file as opposed to zero charge itp?When creating the tpr file for energy minimisation:gmx_mpi grompp -f em.mdp -c graphene_.gro -n system.ndx -o topol.tprI received this:System has non-zero total charge: 30.5944.Total charge should normally be an integer.Will the partial charge of graphene affect the NVT run, apart from slowing it down?Regards,Kester
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Re: [gmx-users] Creating an ITP file for charmm27

[Justin Lemkul]

On 9/2/14, 10:13 PM, Kester Wong wrote:

Dear gmx-users,


I have manually created a graphene.itp file for charmm27 forcefield
calculations, with the intention to model the contact angle of water.

The atomic mass and charge values were obtained from the forcefield 
ffnonbonded.itp.

Could anyone please advise if my file is correct?


[ moleculetype ]

;name nrexcl

GRA   3

[ atoms ]

; id   at type   resnum resname atname cg no charge mass

1   C  1 GRA   C 1  0.5112.011

2   C  1 GRA   C 2  0.5112.011

3   C  1 GRA   C 3  0.5112.011

4   C  1 GRA   C 4  0.5112.011

5   C  1 GRA   C 5  0.5112.011

6   C  1 GRA   C 6  0.5112.011

7   C  1 GRA   C 7  0.5112.011

8   C  1 GRA   C 8  0.5112.011

9   C  1 GRA   C 9  0.5112.011

   10   C  1 GRA   C10  0.5112.011

   11   C  1 GRA   C11  0.5112.011

   12   C  1 GRA   C12  0.5112.011

   13   C  1 GRA   C13  0.5112.011

   14   C  1 GRA   C14  0.5112.011

   15   C  1 GRA   C15  0.5112.011

   16   C  1 GRA   C16  0.5112.011

   17   C  1 GRA   C17  0.5112.011

   18   C  1 GRA   C18  0.5112.011

   19   C  1 GRA   C19  0.5112.011

   20   C  1 GRA   C20  0.5112.011

   21   C  1 GRA   C21  0.5112.011

   22   C  1 GRA   C22  0.5112.011

   23   C  1 GRA   C23  0.5112.011

   24   C  1 GRA   C24  0.5112.011

   25   C  1 GRA   C25  0.5112.011

   26   C  1 GRA   C26  0.5112.011

   27   C  1 GRA   C27  0.5112.011

   28   C  1 GRA   C28  0.5112.011

   29   C  1 GRA   C29  0.5112.011

   30   C  1 GRA   C30  0.5112.011

   31   C  1 GRA   C31  0.5112.011

   32   C  1 GRA   C32  0.5112.011

   33   C  1 GRA   C33  0.5112.011

   34   C  1 GRA   C34  0.5112.011
   35   C  1 GRA   C35  0.5112.011
   36   C  1 GRA   C36  0.5112.011
   37   C  1 GRA   C37  0.5112.011
   38   C  1 GRA   C38  0.5112.011
   39   C  1 GRA   C39  0.5112.011
   40   C  1 GRA   C40  0.5112.011
   41   C  1 GRA   C41  0.5112.011
   42   C  1 GRA   C42  0.5112.011
   43   C  1 GRA   C43  0.5112.011
   44   C  1 GRA   C44  0.5112.011
   45   C  1 GRA   C45  0.5112.011
   46   C  1 GRA   C46  0.5112.011
   47   C  1 GRA   C47  0.5112.011
   48   C  1 GRA   C48  0.5112.011
   49   C  1 GRA   C49  0.5112.011
   50   C  1 GRA   C50  0.5112.011
   51   C  1 GRA   C51  0.5112.011
   52   C  1 GRA   C52  0.5112.011
   53   C  1 GRA   C53  0.5112.011
   54   C  1 GRA   C54  0.5112.011
   55   C  1 GRA   C55  0.5112.011
   56   C  1 GRA   C56  0.5112.011
   57   C  1 GRA   C57  0.5112.011
   58   C  1 GRA   C58  0.5112.011
   59   C  1 GRA   C59  0.5112.011
   60   C  1 GRA   C60  0.5112.011


In the tutorial by Andrea Minoia (http://chembytes.wikidot.com/grocnt), all the
charges of graphene were set to zero, but I have decided to keep the graphene
surface charges.

Has anyone looked at the difference between the water/graphene interaction,
having a charged graphene .itp file as opposed to zero charge itp?


When creating the tpr file for energy minimisation: gmx_mpi grompp -f em.mdp  -c
graphene_.gro -n system.ndx -o topol.tpr


I received this:  System has non-zero total charge: 30.5944. Total charge
should normally be an integer.

Will the partial charge of graphene affect the NVT run, apart from slowing it 
down?



The charges are unreasonable.  The charges you find in ffnonbonded.itp have no 
general meaning aside from the specific functional group from which they were 
pulled.  You're using the wrong atom types and charges, having taken both from 
carbonyl carbon parameters.  You should be using CA (aromatic carbon) with zero 
charge on each.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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 mearg Ligand protein and Lipid

[RINU KHATTRI]

hello justin
i made tc_group for protein ligand and popc but i have  merged
protein_ligand_popc and sol_cl  i made only two group now im running
long simulation what can i do is this two  tc_group can create the
wrong analysis.
kindly help


On Wed, Sep 3, 2014 at 3:42 AM, Justin Lemkul jalem...@vt.edu wrote:


 On 9/2/14, 10:52 AM, neha bharti wrote:

 Hello All

 I am trying to perform MD for protein ligand protein complex in popc lipid
 with
 charmm36 force field and also follow Justin A. Lemkul tutorial.

 I also wanted to ask that while create special index groups consisting of
 solvent + ions and protein + lipids using make_ndx if i am having a system
 with ligand molecule also then should I add it with protein lipid complex
 or add it separately with protein like

 16 | 14 to merge the SOL and CL groups

 1 | 13 | to merge Protein and POPC groups

 and
 1 | 12 to merge Protein and LIGAND groups

 or I can add them like 1 | 12 | 13 to merge Protein and LIGAND and POPC
 groups


 Yes, this is the proper way to merge three groups.

 I would likely create 3 tc-grps: protein+ligand, lipids, and solvent+ions.

 -Justin

 --
 ==

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

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 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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