Re: [gmx-users] Lipid head movement normal to monolayer.

Hey, I'm not sure about lipid headgroups "emersing" "into water". Maybe calculate the average and individual positions of the P and/or N atoms in the z axis for each frame. It's normal that there are some fluctuations though. Anyways, if you want to compare the movement of each lipid molecule in

Re: [gmx-users] Simulation queries

Hi 1) Make sure that when you replace "HEM" by "HEME" you keep the same spacing, e.g. `sed 's/HEM /HEME/g' input.pdb > output.pdb` (as opposed to `sed 's/HEM/HEME/g' input.pdb > output.pdb`). If the spacing is not correct it won't work. 2) No 3) Charmm36 should work just fine if you rename the c

Re: [gmx-users] usage trjconv in membrane simulation

Hi Mije, Maybe check this: http://www.gromacs.org/Documentation/Terminology/Perio dic_Boundary_Conditions?highlight=trjconv As described 'there is no magic "do what I want" recipe', so you'll have to try different options till you find a sequence that works for you. Mine is the following: 1) -p

Re: [gmx-users] Questions Regarding principal components analysis

Hi, 1) Short answer is no. The simplest PCA using GROMACS tools is perhaps cartesian PCA using g_covar and g_anaeig. 2) Highly depends on the size of your system, its dynamics, and what you are trying to characterise using PCA. I recommend you to study this topic a little bit further before perf

Re: [gmx-users] Membrane cutt-offs

Hi, Just check the paper corresponding to the lipid force field you want to use. Cheers, On 6 February 2017 at 06:41, Neda Rafiee wrote: > Hi! > I have a question regarding to cut-off values for membranes. I know that > using usual cut-offs is not appropriate for systems including membrane. >

Re: [gmx-users] question

Hi Álvaro, What does "it gets water" mean? During the simulation? If yes, check some membrane properties (e.g. area per lipid mainly, thickness, etc...) and compare with previously reported (experimental and computational) values. That's not supposed to happen in equilibrated membrane bilayers.

Re: [gmx-users] 1-4 interaction parameters in GROMOS 54a7

Hi Faust, Check the following references: - Schmid_2011_EBJ - Oostenbrink_2004_JCC Hope this helps. Cheers, On 27 Se

Re: [gmx-users] energy minimization

Hi Surya, I'm not sure I understand what you want to do. Do you want to energy minimise an entire trajectory? After the production phase? Why? The -c flag in mdrun is the output, the last conformation sampled during the mdrun. You can use this output file as the input structure for an energy mini

Re: [gmx-users] Accelerated MD in GROMACS

Hi, What do you mean by "it gives more predicable results compared to flooding"? I was actually going to propose that option. If anything, the flooding potential applied in conformational flooding is more meaningful than a non-specific boost potential (to the dihedral and/or total potential) that

Re: [gmx-users] Simulation in Constant pH simulation ...

Just to clarify. What Justin is suggesting is not a constant-pH MD simulation (as the protonation states won't be allowed to change during the simulation as explained), but it might be a good starting point to understand if different (fixed) protonation states will affect the properties of your sy

Re: [gmx-users] Simulation in Constant pH simulation ...

Nikhil, You might want t check this link to start with: http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation. Also a simple google search "GROMACS Constant pH MD" should give you some idea of the available options. Regards, On 15 June 2016 at 16:08, Nikhil Maroli wrote: > Dear

Re: [gmx-users] How to run gromacs on gpu?

Hi Shahab, Maybe check GROMACS documentation --> http://www.gromacs.org/Documentation/Acceleration_and_parallelization#CPU_acceleration.3a_SSE.2c_AVX.2c_etc Cheers, On 14 June 2016 at 10:42, shahab shariati wrote: > Dear all, > > How to run gromacs on gpu? > > Which command is required? mdrun?

Re: [gmx-users] Checking PMF convergenece using WHAM

Hey Khuong, These might help: - http://pubs.acs.org/doi/abs/10.1021/ct100494z - http://pubs.acs.org/doi/abs/10.1021/jp9110794 Regards, On 17 May 2016 at 01:59, Khuong Truong Gia wrote: > Dear all, > > I need your help about how to check the PMF convergence. Can you guys show > me how to ch

Re: [gmx-users] Selection syntax in make.ndx

James, Please try spending some time learning how to use GROMACS tools. Just because there's a mailing list it doesn't mean that you shouldn't try figuring things out by yourself beforehand. This is far too basic! 1. Protein 2. Chain A > 1 && ! 2 On 29 April 2016 at 11:44, James Starlight wro

Re: [gmx-users] Analysis of the protein-protein binding

Hi James, Trajectory analysis are highly dependent on the system of study, namely on what you want to get from your simulations. Also, the protocol you described is a fairly common one. Having said that, a good strategy is probably starting by checking the literature for ways to caracterize bindin

Re: [gmx-users] distance restraint between 2 molecules

Hi Hong, You have (at least) two options: 1) Edit the specbond.dat file so that the pdb2gmx creates a covalent bond between the ligand and the protein (the bonded terms for this interaction have to be present in the force field files); 2) Use position restrains on these two atoms instead. Chose

Re: [gmx-users] RMSD calculation of protein-ligand complex

Hi, You can create a group with the protein and the ligand using the make_ndx tool. Then you can use the created index file as input for your rmsd calculation. Cheers, On 22 Apr 2016 10:47, "Aswathy soman" wrote: > Hi, > I have done a 100 ns simulation of protein-ligand complex. I was wondering

Re: [gmx-users] Regarding 2D simulation

Go to http://manual.gromacs.org/online/mdp_opt.html and search for "pbc". On 11 March 2016 at 05:22, Raju Lunkad wrote: > Dear all Gromacs users, > > I am running the simulation using pbc in 2 directions instead of all > directions. For example, pbc = xy instead of pbc = xyz. > Kindly tell

Re: [gmx-users] area per lipid of POPS/POPC mixed bilayer

Hi Kamakshi, Maybe you should start by reading some literature on membrane simulations and POPC/POPS mixtures. You are basically asking GROMACS users to do your work for you. If you built the membrane yourself (in opposition to using a pre-equilibrated membrane patch), at least run it for 100 ns.

Re: [gmx-users] Embedding Protein into lipid bilayer

l. On 19 February 2016 at 10:15, Catarina A. Carvalheda dos Santos < c.a.c.dossan...@dundee.ac.uk> wrote: > Hi Ali, > > First create the topology for the protein alone using pdb2gmx. > > Then, and if you already have a pre-equilibrated membrane patch, perform > the protein al

Re: [gmx-users] Embedding Protein into lipid bilayer

Hi Ali, First create the topology for the protein alone using pdb2gmx. Then, and if you already have a pre-equilibrated membrane patch, perform the protein alignment and insertion into the membrane. There are several ways to do this (see below). Align the protein with the membrane: - manual proc

Re: [gmx-users] Introduction of mutation into a PDB file, how?

Hi Seera, This is not a GROMACS related question. Try PyMOL (Wizard-->Mutagenesis). Cheers, On 16 February 2016 at 09:10, Seera Suryanarayana wrote: > Dear Gromacs users, > > I would like to introduce mutation into a pdb file which is going to be > used for md simulations. Kindly suggest me t

Re: [gmx-users] How to visualizing gro file in pymol

Hi Anu, You can always use ediconf to convert your .gro file into a .pdb file =) For multiple chain systems Pymol needs the chain information in the structure file. Because .gro files don't have the chain info, you'll always need a .pdb file. If this is your case, that's the reason why the cartoo

Re: [gmx-users] trjconv - two chains are separated

Hi there, I had similar problems in the past. You'll have to play with trjconv and find the best combination of different flags to solve the visualization problem. You can start by trying out this workflow for example: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Re: [gmx-users] How to get an index file containing non polar atoms in gromacs?

I think you can figure this out after playing 5 min with the make_ndx tool, but here it goes: "r ILE | r LEU | r VAL" will select all the isoleucines, leucines and valines in your system. Cheers, On 25 January 2016 at 12:23, Shima ebrahimi wrote: > > > Dear Users, > > I want to determine hydr

Re: [gmx-users] Serine phosphorylation

Yes, Peter is right. I was assuming the residue S2P is already in the amber force field. If not, you can use the phosphoserine parameters derived by Homeyer and co-workers and distributed in the AMBER parameter database

Re: [gmx-users] Serine phosphorylation

Hi Simone, You can simply build the serine phosphoryl group (PO3) using PyMOL or any other graphics system that allows you to do this. In case of PyMOL you can easily find instructions online. Avoid clashes with other atoms or you'll have problems while minimising the system. Change the name of t

Re: [gmx-users] POVPC MARTINI ff

nks for your reply. > > > > > > That weblink, however, is not working. > > > > > > Is there somewhere else I can look. > > > > > > CHARMM GUI MARTINI membrane builder also does not have POVPC MARTINI > ff. > > > > > >

Re: [gmx-users] POVPC MARTINI ff

> Thanks, > sxn > > > > > > On Thu, Dec 17, 2015 at 4:43 AM, Catarina A. Carvalheda dos Santos < > c.a.c.dossan...@dundee.ac.uk> wrote: > > > Hi Shivangi, > > > > Check the Lipidbook @ http://lipidbook.bioch.ox.ac.uk > > > >

Re: [gmx-users] Help with editconf

This is a very silly question, but I have to ask. In your coordinates file (.gro or .pdb, option -f in the make_ndx tool) you have the protein and the lipids, right? On 17 December 2015 at 15:12, Catarina A. Carvalheda dos Santos < c.a.c.dossan...@dundee.ac.uk> wrote: > Rita, > &g

Re: [gmx-users] Help with editconf

ta > > No dia 17/12/2015, às 11:27, "Catarina A. Carvalheda dos Santos" < > c.a.c.dossan...@dundee.ac.uk> escreveu: > > > Consider the following groups in an imaginary .ndx file: > > > > 0 Protein > > 1 Lipid_1 > > 2 Lipid_2 > > 3

Re: [gmx-users] Help with editconf

Consider the following groups in an imaginary .ndx file: 0 Protein 1 Lipid_1 2 Lipid_2 3 Lipid_3 4 SOL To create a new group with the protein and the 3 types of lipids using make_ndx: 0 | 1 | 2 | 3 This will create a new group containing groups 0, 1, 2 and 3. On 17 December 2015 at 11:13, Rita

Re: [gmx-users] POVPC MARTINI ff

Hi Shivangi, Check the Lipidbook @ http://lipidbook.bioch.ox.ac.uk Cheers, On 17 December 2015 at 04:14, shivangi nangia wrote: > Hello All, > > I am looking for MARTINI ff for POVPC, its not on MARTNI webpage. > > It will be great if anyone can help me with it. > > Thanks in advance. > > Rega

Re: [gmx-users] problem with equilibration of DLiPC membrane

doable. > > All the best, > > Shiva > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Catarina > A. Carvalheda dos Santos > Sent: Thursday, November 12, 2015 11:03 AM >

Re: [gmx-users] problem with equilibration of DLiPC membrane

> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Catarina > A. Carvalheda dos Santos > Sent: Thursday, November 12, 2015 1:44 AM > To: Discussion list for GROMACS users > Cc: gromacs.org_gmx-users@

Re: [gmx-users] problem with equilibration of DLiPC membrane

The phase transition temperature of DLiPC is -57 degrees (around 216 K) according to this table... On 11 November 2015 at 18:48, Shiva Emami wrote: > > > > Dear all, > > I'm a new Gromacs u

Re: [gmx-users] using charmm36 force field with gromacs

Thank you Justin. On 5 November 2015 at 15:30, Justin Lemkul wrote: > > > On 11/5/15 5:33 AM, Catarina A. Carvalheda dos Santos wrote: > >> Thank you very much! >> >> Is it possible to add this information about the proper use of constraints >> in CHARMM

Re: [gmx-users] using charmm36 force field with gromacs

gt; Mark >> >> On Wed, Nov 4, 2015 at 1:14 PM Justin Lemkul wrote: >> >> >>> >>> On 11/4/15 4:52 AM, Catarina A. Carvalheda dos Santos wrote: >>> >>>> Hi Justin, >>>> >>>> Regarding the nonbonded settings for protein-membrane

Re: [gmx-users] using charmm36 force field with gromacs

Hi Justin, Regarding the nonbonded settings for protein-membrane simulations using CHARMM. The information you provided used to be available at http://www.

Re: [gmx-users] Simulations of proteins in membrane bilayer

Hey, If that doesn't do the trick use the flags suggested by Terry and also '-ur compact'. This works for me. Regards, On 1 October 2015 at 02:49, Terry wrote: > Hi, > > Try options '-pbc mol -center' with the gmx trjconv tool. > > Terry > > > On Thu, Oct 1, 2015 at 4:48 AM, 凌未风 wrote: > > >

Re: [gmx-users] mutating the protein

Hi there, I don't know about other options, but PyMOL allows you to do this using the "Mutagenesis Wizard" (just google it and you'll find step-by-step instructions in the PyMOL Wiki). Whatever you use, make sure that you select a proper side chain orientation (rotamer) when performing the mutatio

Re: [gmx-users] addition of hydronium ion in simulation box

Regarding CpHMD methods, I would just like to add that you have, in fact, several options. In case you are interested, there is a good summary on subject @ http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation. Regards, On 22 September 2015 at 06:59, Groenhof, Gerrit wrote: > Hi,

Re: [gmx-users] Using TIP4P(2005) with GROMOS-53a6

Hi, Smith is right. 53A6 was parametrized using the SPC water model: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20090/abstract. Regards, On 14 September 2015 at 14:44, Smith, Micholas D. wrote: > As far as I am aware, GROMOS53A6 does not play nice with water models > other than SPC/E > > =

Re: [gmx-users] get dihedrals in 0 to 360 degrees instead of -180 to +180 degrees

Hi again, Actually what I said is wrong. The right way to do it is: awk '{print $1, ($2<0) ? $2+360 : $2}' Sorry about that. On 10 September 2015 at 12:07, GAYATHRI S wrote: > Thank you very much. > That was helpful. > > Regards, > Gayathri S. > > > > > Hi, > > > > I'm assuming you are meas

Re: [gmx-users] get dihedrals in 0 to 360 degrees instead of -180 to +180 degrees

Hi, I'm assuming you are measuring more than one dihedral (since you are using the -all option). So assuming columns 2 to 5 correspond to the measured dihedrals: awk '{print $1,($2+180),($3+180),($4+180),($5+180)}' angaver.xvg > new_ angaver.xvg This should do the trick. Regards, On 10 Septe

Re: [gmx-users] Membrane protein insertion/orientation methods

Hi there, Lambada + InflateGRO2 is a good combination. As for which method is the best one is difficult to say. If you read the articles you will have a nice idea of the pros and cons of each method and then you can decide by yourself. The only thing I can say is that after reading them all I wen

Re: [gmx-users] Topology for DOPC lipid Charmm36 ff

Hi Phan, DOPC is already in the Charmm36 distribution for GROMACS. Check the .rtp file. Cheers, On 7 August 2015 at 05:51, Vy Phan wrote: > Dear Gromacs users, > I want to run tranmembrane protein with Gromacs code and using Charmm 36 > ff. I tried to search the the topology for DOPC, I could

Re: [gmx-users] Mdrun and minimum image convention

ernal monitor works pretty well. > Trying to include it in the MD code adds clutter there and further burdens > maintenance. And doing such calculations at every frame also adds a > significant cost. > > Cheers, > > Tsjerk > On Apr 15, 2015 6:23 PM, "Catarina A.

Re: [gmx-users] Mdrun and minimum image convention

Thank you for the clarification Mark. Would you consider to add such feature (as an mdrun flag for example: -pi ) in the next GROMACS versions? On 15 April 2015 at 17:12, Mark Abraham wrote: > Hi, > On 15/04/2015 3:55 pm, "Catarina A. Carvalheda dos Santos" < > c.a.c.

[gmx-users] Mdrun and minimum image convention

Hi there, Is there any way to control the minimum distance with periodic images during mdrun and exit the simulation automatically if this distance is equal or lower than the user-defined cutoff? I know that this can be monitored with g_mindist, but doing it automatically would avoid wasting simul

Re: [gmx-users] Replicating and equilibrating DPPC 128 lipid. pdb

> compressibility = 4.5e-5 4.5e-5 > ref_p = 1.0 1.0 > constraints = all-bonds > > I get LINCS error message. > But if i use NONE option for contsraints, i get results. Is it the right > way of doing it? > > On Wed, Nov 19, 2014 at 4:17 PM, Catarina A. Carvalheda dos Sant

Re: [gmx-users] Replicating and equilibrating DPPC 128 lipid. pdb

Hi Priya, You can use genconf with the option -box to replicate your box (in this case your membrane) as many times as you want in the x,y and z directions. Keep in mind that -box only deals with integers (number of boxes), so something like "-box 1.5 2.5 1" will be equivalent to "-box 2 3 1". If