Re: [gmx-users] membrane protein simulation

63.com> wrote: > Dear Tsjerk, > > Thanks for the reply. Will you please introduce to me sevral membrane > builders whith results compatible with gromacs, especially on-line > available membrane builders? > > Best regards. > > Brett > > > > > > >

Re: [gmx-users] Extracting Trajectory and False Simulation

Hi Rabindra, You can do an mdrun -rerun with the original trajectory and the alternative topology. Cheers, Tsjerk On Mon, Sep 7, 2015 at 6:32 AM, Rabindra Raj Oliya wrote: > Actually I have two topology files corresponding to ideal and real system. > Initially I have

Re: [gmx-users] When is it necessary to use the -nopbc option in GROMACS analysis tools (i.e. g_sas)?

Only if you do fitting. Cheers, Tsjerk On Thu, Sep 3, 2015 at 2:08 PM, Justin Lemkul wrote: > > > On 9/3/15 5:23 AM, Bernhard Reuter wrote: > >> Dear all, >> >> Is it necessary to use the -nopbc option ("By default, periodic boundary >> conditions are taken into account, this

Re: [gmx-users] accessing pressure components from trajectory file

p 1, 2015 at 11:25 PM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: > > > Hi Aishwary, > > > > Those components will be in the energy file if you do anisotropic > pressure > > coupling. You can't retrieve them from the trajectory, although you can > > r

Re: [gmx-users] accessing pressure components from trajectory file

Hi Aishwary, Those components will be in the energy file if you do anisotropic pressure coupling. You can't retrieve them from the trajectory, although you can rerun the trajectory to obtain them. Cheers, Tsjerk On Tue, Sep 1, 2015 at 7:48 PM, Aishwary Shivgan < aishwaryshivga...@gmail.com>

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

Hi Yasser, InflateGRO and g_membed do not predict the insertion or orientation, but require the protein to be oriented already. With InflateGRO2, Christian Kandt also brought out LAMBADA which may help aligning a protein with the membrane. memembed is also an orientation predictor. However, I

Re: [gmx-users] conformational entropy with/without jumps

Hi Ahmet, Have you looked at the trajectories? Is the molecule really whole/centered? Cheers, Tsjerk T On Wed, Aug 19, 2015 at 3:32 PM, Ahmet Yıldırım ahmedo...@gmail.com wrote: Dear users, I am trying to get the conformational entropy of some structures but the results I got are

Re: [gmx-users] calculating single atom changes along the trajectory as a measure of distance

Hi Pavan, The distance from an atom to itself is zero by definition. Also, distance in only defined between things, so, indeed, you need two groups for gmx dist. If you mean distance over PBC it's a different matter. Then you want the distance between a group and any of its periodic images.

[gmx-users] re: calculating single atom changes along the trajectory as a measure of distance

Hi Pavan, Please don't reply to a digest, at least not without editing the subject. And remove everything that is not relatsd to what you're replying to. Maybe the answer was what you were looking for, but you expected it in a different form. The distance from a given reference position is

Re: [gmx-users] MD simulations

Hi :) The error is that there are warnings. Well, one warning. A warning from grompp may indicate an inconsistency in the topology (like atom name mismatch), an incompatibility of MDP parameters which grompp corrects automatically (nst*), or a possible pitfall (like too many temperature coupling

Re: [gmx-users] -d for all boxtypes

Hi Sana, Yes, it's pretty much one value to put them all and in the PBC system separate them. Except for the rectangular box, the box is set up based on the circumscribed radius of the solute dilated with the distance d. For the rectangular box it's based on the extent of the protein in x/y/z.

Re: [gmx-users] difference between steep and cg

Hi Ming Tang, See https://en.m.wikipedia.org/wiki/Gradient_descent It has a further link to CG. Cheers, Tsjerk On Jul 11, 2015 4:10 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear Gromacs experts, I am quite confused about the difference between the energy minimization algorithm steep and

Re: [PyMOL] spectrum and the default minimum and maximum values

Hi Emily, No, it takes them from the selection. Cheers, Tsjerk On Jul 7, 2015 4:09 PM, Emilia C. Arturo (Emily) ec...@drexel.edu wrote: To be extra clear/redundant: The default value passed is None. If Pymol finds that the argument is None, it takes the minimum/maximum value from the

Re: [PyMOL] spectrum and the default minimum and maximum values

Hi Emily, The default value passed is None. If Pymol finds that the argument is None, it takes the minimum/maximum value from the list of values, otherwise it will take the value provided. The interpolation is indeed linear. Hope it helps, Tsjerk On Tue, Jul 7, 2015 at 4:11 AM, Emilia C.

Re: [gmx-users] on trjcat command

Right. Note that trjcat can also convert the file format. Cheers, Tsjerk On Jul 5, 2015 9:32 AM, Brett brettliu...@163.com wrote: Dear All, The command trjcat can be used for connection of trr files and xtc files in the similar manner, and suppose the first MD is from 0 to 1 ns, the

Re: [gmx-users] VOlume of box

Hi Anik, In NVT the box doesn't change. The volume of the box is the product of the first three numbers of the last line of a GRO file. gmx energy can also extract the system volume if you run in NpT. Cheers, Tsjerk On Tue, Jun 30, 2015 at 11:21 AM, Anik Sen anik@kemi.uu.se wrote: Dear

Re: [gmx-users] Biphasic Systems for BSA

Hi, Actually no, you may be better off with a hexagonal prism, or even a rhombic dodecahedron, which has a hexagonal base too. Oh, and that structure of BSA is a dimer, while the biological unit is a monomer... Cheers, Tsjerk On Jun 27, 2015 7:20 PM, Justin Lemkul jalem...@vt.edu wrote: On

Re: [gmx-users] .xtc and .trr file is missing

Hi RJ, For an XTC file, you need to set nstxtcout (GMX 4.x) or nstxout_compressed (GMX 5). A TPR file is a run _input_ file and is not generated as output. Cheers, Tsjerk On Mon, Jun 22, 2015 at 6:11 AM, RJ ra...@kaist.ac.kr wrote: Dear gmx. I run 100ns simulation of my protein with

Re: [gmx-users] confusion on NPT MD simulation

Hi Ming Tang, You don't need a huge force constant to keep it fixed. Too high forces may give instabilities. And a more gentle one (100-1000) does the trick as well. Cheers, Tsjerk On Jun 17, 2015 4:17 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear Justin, Thank you so much. There are

Re: [PyMOL] efficiency assigning b-factors

Hi Jordan, Yes, although I don't have the answer at hand, it has been given on the user list several times. You can find it in the archives. Cheers, Tsjerk On Jun 16, 2015 08:16, Jordan Willis jwillis0...@gmail.com wrote: Hi, I have a dictionary that has a bunch of values I want to assign

Re: [PyMOL] efficiency assigning b-factors

everyone is pointing to this ( http://www.pymolwiki.org/index.php/Color#Reassigning_B-Factors_and_Coloring) which I somehow missed. However, they seem to be altering one residue at a time like I’m doing. Jordan On Jun 15, 2015, at 11:59 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Jordan

Re: [gmx-users] how to superimpose protein in frames?

trjconv -fit rot+trans T. On Fri, Jun 12, 2015 at 2:37 PM, Albert mailmd2...@gmail.com wrote: Hello: I am just wondering is it possible to superimpose the protein backbone in each frame? I try to do this by command: trjconv -f md.xtc -s md.tpr -pbc res -center when it pop up options for

Re: [gmx-users] Problem in energy minimization

Hi Jin, Can you give the protocol you used in commands? And what are the box dimensions and how many solvent molecules were added? Cheers, Tsjerk On Jun 5, 2015 08:30, Jin J.C jcjin.hcmut@gmail.com wrote: Dear Justin, I have tried to change the box size, make it smaller a little, solvate

Re: [gmx-users] Center of mass motion removal

and the simulation can not run. I think comm-mode =None and {comm-mode =Linear , nstcomm nststeps) is similar meaning. I misunderstand something? Could you explain more? Many Thanks Tuong Vy 2015-06-03 15:11 GMT+09:00 Tsjerk Wassenaar tsje...@gmail.com: Hi Tuong Vy, Right. If COMM

Re: [gmx-users] Center of mass motion removal

Hi Tuong Vy, Right. If COMM is removed every N steps and the simulation runs for M N steps, then COMM will never actually be removed. Cheers, Tsjerk On Jun 3, 2015 4:44 AM, Vy Phan phanvy120...@gmail.com wrote: Dear all, I wonder when I set the comm-mode =Linear , and nstcomm (frequency

Re: [gmx-users] fix COM of a group

Hi Ming Tang, comm_mode = Linear comm_grps = CA Cheers, Tsjerk On Wed, Jun 3, 2015 at 9:34 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear all, Is there any method that can fix the center of mass of a group of atoms? I create a group containing CA atoms of the first residue in each of the

Re: [gmx-users] fix COM of a group

0 0 0 1 3 1919 -1.542 nm -1.542 nm Can I just ignore them? Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar

Re: [gmx-users] URGENT query regarding pbc = no in grompp in membrane simulations

Why is this urgent? Have you tried the suggestions given by the program? Cheers, Tsjerk On Wed, Jun 3, 2015 at 12:08 PM, Antara mazumdar antara.mazum...@igib.in wrote: i want to simulate a system having membrane and proteins with pbc=no to allow surface effects. I use the following settings

Re: [PyMOL] time bar in a movie done with pymol

Hi Stéphane, You could use four pseudoatoms A,B,C,D and have bonds between A/B and C/D. Then you show them as sticks with A/B in red and C/D in white and let B+C move from position A to position D. Alternatively, you can use CGO. Cheers, Tsjerk On Wed, May 27, 2015 at 3:30 PM, ABEL Stephane

Re: [gmx-users] Is it reasonable to get a bad Ramachandran plot after MD?

Hi Kevin, What happens if you bring the temperature down gradually to experimental (crystallization) conditions? For each residue, what is the proportion of time spent in 'forbidden' regions? Is there a correlation with B-factor? And what would be the effect of the outliers on the experimental

Re: [gmx-users] Renaming of the chains in time of simulation (like ABC...to X)

Hi Nil, The .gro file does not contain chain information. You can use the .tpr file, or convert the .tpr file to PDB format and use that in stead of the .gro file. Cheers, Tsjerk On Tue, May 26, 2015 at 5:38 AM, Ambarnil Ghosh ambargrom...@gmail.com wrote: Hi Mark and GROMACS users, Thanks

Re: [PyMOL] how to highlight some residues and make other residues being as background?

Hi Yeping Sun, In such cases, I usually use light colors with little contrast (white, wheat, grey, pastel) for the surroundings (on a white background) and bright, contrasting colors (chartreuse, orange, hotpink, marine) for what you want to highlight. In addition, you may want to play around

Re: [PyMOL] on color based on b-factor spectrum

Hi Smith, The colors are interpolated linearly from the minimum to the maximum value. 'spectrum' allows specifying the extreme values, which is handy when you need a symmetric scale. If you color green_yellow_blue, you get a green to yellow gradient from min to (min+max)/2 and a yellow to blue

Re: [gmx-users] pdb2gmx: Can I change the margin 10% to a higher value in the specbond.dat ?

Hi Cheng, You can add another entry for a disulfide bond with a different length. Cheers, Tsjerk On Thu, May 21, 2015 at 11:31 AM, Zhang, Cheng c.zhang...@ucl.ac.uk wrote: Dear GROMACS experts, I am using pdb2gmx for a protein with 5 disulfind bond https://copy.com/kPLlSianI4LtohNy

Re: [gmx-users] Gromacs Error

Hi Manoj, The error is clear. Check the settings referred to in your .mdp file and modify them accordingly. Cheers, Tsjerk On May 19, 2015 07:35, manoj damale manojaurangabad...@yahoo.co.in wrote: Dear All, i'm geting below error while subjecting my system (Protein-ligand) for equlibriation

Re: [gmx-users] Gromacs Error

Bengal State, India. On Tuesday, 19 May 2015 11:32 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Manoj, The error is clear. Check the settings referred to in your .mdp file and modify them accordingly. Cheers, Tsjerk On May 19, 2015 07:35, manoj damale manojaurangabad

Re: [gmx-users] The octahedron problem

Hi Tuong Vy, An octahedral or dodecahedral box is pretty tricky. I have a Pymol script for generating them, but it will probably require some more work... Cheers, Tsjerk On May 19, 2015 13:18, Vy Phan phanvy120...@gmail.com wrote: Dear Gromacs Users, I have the problem with generating the

[gmx-users] Fwd: Re: Gromacs Error

To: Tsjerk Wassenaar tsje...@gmail.com Cc: Dear, Sorry to distrub you, when i have replace rcoulomb= 1.4 ; short-range electrostatic cutoff (in nm) with rcoulomb must be = rlist ; short-range electrostatic cutoff (in nm) it again giving error as WARNING 1 [file nvt.mdp, line

Re: [gmx-users] The octahedron problem

Hi Tuong Vy, No, it uses Pymol CGO to draw the cell. I think that won't work in VMD. Cheers, Tsjerk On May 19, 2015 15:28, Vy Phan phanvy120...@gmail.com wrote: Dear Tsjerk Wassenaar Can I display it on the VMD ? Thank a lot Tuong Vy 2015-05-19 20:22 GMT+09:00 Tsjerk Wassenaar tsje

Re: [PyMOL] sticks do not connect to the backbone

Hi Yeping Sun, Try: set cartoon_flat_sheets, 0 set cartoon_smooth_loops, 0 Cheers, Tsjerk On Mon, May 18, 2015 at 10:23 AM, sunyeping sunyep...@aliyun.com wrote: Dear all, I find that when I show the protein as cartoon representation in pymol, and select some residues to show as

Re: [gmx-users] energy minimization problem

Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote: Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated

Re: [gmx-users] energy minimization problem

. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi

Re: [gmx-users] increasing simulation time via temperature rising

Hi Nazli, No, that's not related to temperature. Otherwise you'd probably see a trend. I guess with the 600K simulation you have another process that interferes and eats CPU. Mind that a simulation running on four/eight cores will be affected significantly by anything that uses a considerable

Re: [gmx-users] martini issues

There's nothing to add to a perfect answer! Indeed 'p' is for 'polarizable' and should be used with a polarizable water model (PW) and not with the normal model (W). Also, Martini is not Gromacs, so information about the force field should not be expected in the Gromacs manual, but can be found in

Re: [gmx-users] Insane.py problem

Hi Carlos, Use -box 20 20 10, without commas. Cheers, Tsjerk On May 13, 2015 2:25 PM, João Henriques joao.henriques.32...@gmail.com wrote: Dear Carlos, It's actually the other way around, it's trying to convert a string into a float. I am absolutely not familiar with the code or the

Re: [gmx-users] Insane.py problem

of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl On May 13, 2015 at 3:28:52 PM, Tsjerk Wassenaar (tsje...@gmail.com mailto: tsje...@gmail.com) wrote

Re: [gmx-users] How to remove the water molecules?

Hi Surya, Non-Water is a default index group. Just select that when running trjconv. Cheers, Tsjerk On Tue, May 12, 2015 at 8:34 AM, Seera Suryanarayana paluso...@gmail.com wrote: Dear gromacs users I have simulated a protein for 500ns in solvent system. I want to remove water molecules

Re: [PyMOL] how to connect to atoms?

of TehranTehran, Iran* *Email: karami.le...@ut.ac.ir karami.le...@ut.ac.ir karami.le...@ut.ac.ir* *Tel: +98 9193155894 %2B98%209193155894* On Tue, May 12, 2015 at 12:27 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Leila, Please ask this question on the gromacs mailing list. But first

Re: [gmx-users] [PyMOL] how to connect to atoms?

of TehranTehran, Iran* *Email: karami.le...@ut.ac.ir karami.le...@ut.ac.ir karami.le...@ut.ac.ir* *Tel: +98 9193155894 %2B98%209193155894* On Tue, May 12, 2015 at 12:27 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Leila, Please ask this question on the gromacs mailing list. But first

Re: [gmx-users] all-atom pca

-fit). Its like if I try to fit same structures they should exactly overlap. May the fitting algorithm has a glitch when molecule is big as in my case (~ 500 atoms) Thanks Jio On Mon, May 11, 2015 at 10:08 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Jio, You'll have to look

Re: [R] Variance-covariance matrix

) . . . Σ *x*n2 / (N-1) Reference: “Time series and its applications – with R examples”, Springer, $7.8 “Principal Components” pag. 468, 469 Cheers, Giorgio *From:* Tsjerk Wassenaar [mailto:tsje...@gmail.com] *Sent:* domenica 10 maggio 2015 22:11 *To:* Giorgio Garziano

Re: [R] Variance-covariance matrix

Hi Giorgio, For a univariate time series? Seriously? data - rnorm(10,2,1) as.matrix(var(data)) Cheers, Tsjerk On Sun, May 10, 2015 at 9:54 PM, Giorgio Garziano giorgio.garzi...@ericsson.com wrote: Hi, Actually as variance-covariance matrix I mean:

Re: [gmx-users] [pairs] directive issue

Hi Raja, [ pairs ] is a molecule level directive and so has to fall under a [ moleculetype ] directive. If you want to add pair types based on atom types, similar to [ bondtypes ], you'll have to use... [ pairtypes ] Try to get hold of the force field lay out if you're tampering with parameters.

Re: [PyMOL] Is cyclododecene in the database of PyMol?

Hi Rajib Yuktimmana, Cyclododecene has twelve carbon atoms in a ring, and one of the bonds is a double bond. This means that there are two forms, cis and trans. Neither is wrong, if not specified explicitly. For the rest, the structure is very flexible, so there is not a single structure, but

Re: [gmx-users] NVT Equilibration error

Hi Agnivo, What is the rationale for ignoring the long bond warning? Cheers, Tsjerk On May 5, 2015 17:41, Agnivo Gosai agnivogromac...@gmail.com wrote: Dear Users, I have a solvated protein-dna structure placed inside a simulation box. During topology preparation and subsequent steps I did

Re: [PyMOL] cylinder fuzzy color when ray traced

Hey Doug, Does set ray_trace_mode, 3 do what you want? Cheers, Tsjerk On Fri, May 1, 2015 at 5:20 PM, Douglas Kojetin douglas.koje...@gmail.com wrote: Hi All, I am trying to highlight a specific residue (black color) in a helix (orange color) displayed in cylinder mode. When I perform

Re: [gmx-users] Secondary Structure Restraints: martinize.py

Hi sxn, What do you mean with reverse coarse graining? You can specify the secondary structure also as string, which is doable if the peptide is not too long, e.g. using -ss HHHLLL. Otherwise, you can put the secondary structure you want in a simple file, and pass that with the option

Re: [gmx-users] Secondary Structure Restraints: martinize.py

or not. For example, in one of my trials I changed the structure column of the .dssp file from H to nothing hoping once I coarse grain with that modified file I would get a semi secondary structure restrained coarse grained peptide. Thanks, sxn On Fri, May 1, 2015 at 3:59 PM, Tsjerk Wassenaar

Re: [R] DeSolver giving NA as output, but running fully.

Hey :) W2MH = y[43]; #number of infected vaccinated males high risk infected with non-vaccine strain length(y0) [1] 42 As a sidenote, would you mind sharing the flow diagram with me, so I can show it to my students doing a practical with DeSolve, as example of a contemporary

Re: [gmx-users] NMA with gromacs trajectory

Hi Rajan, NMA/GNM is performed on a single structure, not on a trajectory. NMA can be performed with Gromacs, but GNM/ENM is not possible, AFAIK. Cheers, Tsjerk On Apr 28, 2015 5:07 PM, rajan kumar choudhary rajugunju...@gmail.com wrote: ​Dear all, Is it possible to perform Normal mode

Re: [gmx-users] pdb2gmx and periodic molecule

Hi Alex, I think the best way is to extend the chain, such that you get an overlap between both ends. So for a stretch of DNA ACGT You would generate TACGTA Then you strip off the terminal atoms and rewire the links over the boundary. It requires renumbering the topology and at first looks a

Re: [gmx-users] a question related to gmx energy minimization

Hi Brett, Too high for what? You do EM because you just built (part of) your system, and in doing so introduced clashes and non-ideal geometries. These lead to high potential energy, so you relax them with EM. What you see is how much the system relaxed. Noone usually cares how much potential

Re: [gmx-users] Variations of angles in a triclinic box

Hi Antonio, You scale the axes separately. so you may stretch one component of a vector, and/or compress one, thus changing the angle. Cheers, Tsjerk On Wed, Apr 22, 2015 at 4:15 PM, Antonio Pizzirusso antonio.pizziruss...@gmail.com wrote: Dear Gromacs users, Recently I have used NPT

Re: [gmx-users] membrane protein simulation

Hi Mostafa, We have a complete simulation system of bacteriorhodopsin in the purple membrane, which you can use as basis for your simulations if you want. Best, Tsjerk On Apr 22, 2015 10:08 PM, Mostafa Javaheri javaheri.grom...@gmail.com wrote: Dear Justin I am going to simulate a homo

Re: [gmx-users] do_dssp for coarse-grained trajectory

Hi Sandhyaa, DSSP doesn't work on C-alpha only or coarse-grained trajectories. Can you maybe specify what coarse-grain FF you're using? It may be possible to use the tool 'backward' to convert it to atomistic. Cheers, Tsjerk On Tue, Apr 21, 2015 at 6:48 AM, Sandhyaa Subramanian

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

Hi Catarina, I have an MD wrapper that comprises a monitoring mechanism, which allows terminating a simulation after a certain condition is met. Of course, such a mechanism interferes with the MD process, but it will usually add just a bit every so many minutes, checking the results at intervals.

Re: [gmx-users] R-B dihedrals

Hi Alex, Maybe writing out the preprocessed topology (grompp -pp) or checking the .tpr with gmxdump can show whether the dihedral parameters are really what you think they are. Cheers, Tsjerk On Apr 14, 2015 10:32 PM, Alex nedoma...@gmail.com wrote: I have a set of dihedrals described by the

Re: [gmx-users] A query

Hi Priya, Yes, this particular message means that you should also get to know yourself, because it is key to understand others, which is the most important step to not being lonely. This one may not be directly related to the program, but in terms of science, it sort of suggests that you should

Re: [gmx-users] how to modify the files in the force field fold of Gromacs

Hi Ming, Copy the whole folder to your working directory. Gromacs will give force field files in the working directory precedence. Cheers, Tsjerk On Mon, Apr 13, 2015 at 12:32 PM, Ming Tang m21.t...@qut.edu.au wrote: Dear all, I need to modify the .rtp file in charmm27.ff, but I can do

Re: [gmx-users] Can NAMD simulation solve the problem of coordinate clash in a structural model?

Hi Yeping Sun, If the coordinates are garbled (what are serious coordinate clashes?), you'll have a hard time with either NAMD or Gromacs. Cheers, Tsjerk On Mon, Apr 13, 2015 at 6:05 AM, sunyeping sunyep...@aliyun.com wrote: Dear all, I modelled a structural model of a complex containing

Re: [PyMOL] Cartoon visualization of per-residue txt data

according to the B-factor value? Here the issue is with the proper selection E.g PyMOLselect not-relevent, b 0 results only in small atoms selected and PyMOLselect ss, b = 0 Selector-Error: Invalid selection. b-- Regards, James 2015-04-10 21:12 GMT+02:00 Tsjerk

Re: [gmx-users] G_rmsf, reference structur

it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. G_rmsf, reference structure (Eerden, van, F.J.) 2. Re: G_rmsf, reference structure (Tsjerk Wassenaar) 3. Re: GMX-compatible DNA coordinates (Alex) 4. Re: GMX-compatible DNA

Re: [gmx-users] Query- RMSD

No. Cheers, Tsjerk On Apr 7, 2015 12:16 PM, Priya Das priyadas...@gmail.com wrote: Dear all, For checking ligand interactions with protein , i generated a RMSD plot for ligand. The simulations were done for 10 ns. Has the system converged? ​ -- *Let us all join hands to save our

Re: [gmx-users] Query- RMSD

the time for simulation? On Tue, Apr 7, 2015 at 4:16 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: No. Cheers, Tsjerk On Apr 7, 2015 12:16 PM, Priya Das priyadas...@gmail.com wrote: Dear all, For checking ligand interactions with protein , i generated a RMSD plot

Re: [PyMOL] Labelling ligands and amino acids

Hi Brenton, Add a specific atom, at which you want the label, to the selection. You can pick one to get to know its name. Cheers, Tsjerk On Mon, Apr 6, 2015 at 10:03 PM, Brenton Horne brentonho...@ymail.com wrote: Hi, I have skimmed the Label http://pymolwiki.org/index.php/Label page on

Re: [PyMOL] Labelling ligands and amino acids

:28 AM, Tsjerk Wassenaar wrote: Hi Brenton, Add a specific atom, at which you want the label, to the selection. You can pick one to get to know its name. Cheers, Tsjerk On Mon, Apr 6, 2015 at 10:03 PM, Brenton Horne brentonho...@ymail.com wrote: Hi, I have skimmed the Label http

Re: [PyMOL] Zoom animation

Hi Brenton, cmd.zoom(r. pnm, 20) You forgot the quotes: r. pnm Cheers, Tsjerk -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot

Re: [gmx-users] periodic boundary conditions pbc=xyz

Hi Ming, You have another box in your (infinite) periodic system? Cheers, Tsjerk On Sun, Apr 5, 2015 at 10:32 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear all, I did a simulation using periodic boundary conditions pbc=xyz. It turns out that the box is defined too small, and some atoms

Re: [PyMOL] Displaying covalent bonds between amino acids (within protein) and ligand

Hi Brenton, You will also need to show the sticks for the sidechain of residue 62: fetch 1pwc hide show cartoon show sticks, r. pnm show sticks, resi 62 and not name c+n+o Cheers, Tsjerk On Sat, Apr 4, 2015 at 3:52 PM, Brenton Horne brentonho...@ymail.com wrote: Hi, In the structure that

[PyMOL] Fwd: Displaying covalent bonds between amino acids (within protein) and ligand

Oh, and always use 'reply-to-all' if this is follow-up on a post. Cheers, Tsjerk -- Forwarded message -- From: Tsjerk Wassenaar tsje...@gmail.com Date: Sat, Apr 4, 2015 at 9:14 PM Subject: Re: [PyMOL] Displaying covalent bonds between amino acids (within protein) and ligand

Re: [gmx-users] the study of concentration effect in gromacs

Hi Elham, No, a box of 0.5*0.5*0.5 has 0.125 times the volume of one of 1*1*1, so gives an 8 times as high concentration. But it gets more complicated if you mean the concentration of the solution around a protein. I tend to favour using molality (as mol solute per mol solvent) for that. Yes,

Re: [gmx-users] G_rmsf, reference structure

Hi Floris, By default it's A. There is an option for doing B. But B makes no sense. Cheers, Tsjerk On Apr 3, 2015 1:10 PM, Eerden, van, F.J. f.j.van.eer...@rug.nl wrote: Dears, I have calculated the RMSF from a protein trajectory in Gromacs 4.5.5. My question is how the RMSF is

Re: [gmx-users] GMX-compatible DNA coordinates

Hi Alex, You've solved the issue of getting a DNA structure, but now you're facing a problem of getting Gromacs to prune it. That has to do with the naming scheme mainly. Your best bet is using sed to do name substitution. Probably google will give some good hints about such substitutions in PDB

Re: [gmx-users] GMX-compatible DNA coordinates

Hi Alex, Writing a sed oneliner is not the same as writing a renaming script. I commonly use them to process PDB files in some way and it's surprising how much you can do without scripting. Cheers, Tsjerk On Apr 3, 2015 7:13 PM, Alex nedoma...@gmail.com wrote: Gentlemen, Building a script

Re: [gmx-users] the study of concentration effect in gromacs

Hi Elham, You can increase the protein concentration by using a smaller box, or by putting two or more proteins in a box together. With drugs, you can raise the concentration by adding more, using the insert option of genbox. Cheers, Tsjerk On Fri, Apr 3, 2015 at 9:13 PM, elham tazikeh

Re: [gmx-users] GMX-compatible DNA coordinates

Hi Alex, I've done it before, but I can't do it from the top of my head without seeing the input and checking what Gromacs wants. It's not hard work, it's not a lot of work, but it is work, and more than we'll usually consider doing for answering a post on the mailing list. On the other hand, you

Re: [gmx-users] fixed number of clusters from a MD simulation

Hi Rebeca, You'd need to use k-means/k-medians clustering for that, which is not in gmx cluster. I'd suggest to perform PCA and collect the projections onto the first ten or so eigenvectors to decrease the dimensionality. This data matrix you can then process with, e.g., R to perform k-means

Re: [gmx-users] Density of pure tetrolic acid does not agree with experimental data

Hi Nathan, Yes, placement of molecules neglects the interactions. You need to simulate the stuff before drawing conclusions. Cheers, Tsjerk On Mar 31, 2015 8:43 AM, Nathan K Houtz nho...@purdue.edu wrote: Hello Gromacs users, I tried to create a 6.5 nm cubic box of tetrolic acid (otherwise

Re: [gmx-users] Unexpected trjconv -nojump behaviour

Hi Trayder, The first frames did not have the same position/orientation and/or the same box. Cheers, Tsjerk On Mar 31, 2015 10:00 AM, Trayder Thomas trayder.tho...@monash.edu wrote: Hi, I'm struggling with pbc nojump for a particular starting structure and don't understand why. The system

Re: [gmx-users] Unexpected trjconv -nojump behaviour

Hi Trayder, The box is identical (copy+pasted), the orientation varies no more than one would expect frame to frame (membrane protein). There is a 20 A jump between the first and second frame but shouldn't -nojump still be keeping the protein whole? The idea of what jumped may change quite a

[gmx-users] Fwd: A doubt from topology creation in Gromacs

-- Forwarded message -- From: Rakesh Pant rakesh...@live.com Date: Apr 1, 2015 1:13 AM Subject: A doubt from topology creation in Gromacs To: tsje...@gmail.com tsje...@gmail.com Cc: Dear Tsjerk, I got your email id from gromacs user list. I have a doubt from gromacs topology

Re: [PyMOL] Colouring nucleic acids, without changing the colouring of amino acids

Hi Brenton, Jared, For RNA, the residue names are A, C, G, and U (not R*). However it's also possible to specify the nucleic acid, using: set cartoon_color, green, resn G and byres name C1' This way, you filter the selection on an atom of the ribose, that is in all nucleic acids, and in no

Re: [gmx-users] Correlation of dynamics between pairs of residues

Hi, Perhaps defeats the purpose wasn't the right way to say it. But simply plotting the covariance matrices with arbitrary min/max is just an aesthetic thing, so it's not really functional. Hence why no one has coded that. I disagree with that. If you have simulations of the same system

Re: [gmx-users] Extracting frames to a new trajectory based on RMSD cut-off value

Hey :) trjconv also has an option -drop file.xvg with -dropover/-dropunder, which allows writing out frames based on, e.g., RMSD. Cheers, Tsjerk On Tue, Mar 24, 2015 at 1:59 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/23/15 8:32 AM, Sandhyaa Subramanian wrote: Dear all, I have a

Re: [gmx-users] jump problem

Hey :) Cluster the first frame and write out as new reference structure. Then run with that reference, removing jumps. Cheers, Tsjerk On Mar 18, 2015 12:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/17/15 9:03 PM, Ahmet yıldırım wrote: Dear users, I tried to remove the jumps of a

Re: [gmx-users] Placing system at the centre of the box.

, Mar 14, 2015 at 1:38 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Rajan, Do you see the box? From your output it is easily seen that the new center equals 0.5*boxvectors. Cheers, Tsjerk On Mar 14, 2015 5:47 AM, Rajan Kumar kumarrajan...@gmail.com wrote: Hi all

Re: [gmx-users] Placing system at the centre of the box.

Hi Rajan, Do you see the box? From your output it is easily seen that the new center equals 0.5*boxvectors. Cheers, Tsjerk On Mar 14, 2015 5:47 AM, Rajan Kumar kumarrajan...@gmail.com wrote: Hi all, I am trying to study wetting of water on Graphene oxide(GO). My structure has functional

Re: [gmx-users] g_anaeig error inconsistent shifts

Hi Tasneem, So your tpr file doesn't match your trajectory. How come, or why is that? And if your eigenvectors correspond to main chain atoms you can't use protein for analysis. Hope it helps, Tsjerk On Mar 12, 2015 6:07 AM, tasneem kausar tasneemkausa...@gmail.com wrote: for PCA i used the

Re: [gmx-users] g_anaeig error

Hi Tasneem, Please provide a complete workflow, with commands and selections. Cheers, Tsjerk On Wed, Mar 11, 2015 at 10:31 AM, tasneem kausar tasneemkausa...@gmail.com wrote: for PCA i used the g_covar followed by g_anaeig. for g_anaeig i am using the eigenvec.trr file and averagr.pdb file

Re: [gmx-users] Gromacs with InflateGro

Hi Anthony, I'm currently working on an alternative program to put things in an AA membrane. If you want, you can send me the protein (off-list) and I can give it a try. Cheers, Tsjerk On Sun, Mar 8, 2015 at 6:03 PM, Nash, Anthony a.n...@ucl.ac.uk wrote: Hi all, I'm really struggling to

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