Re: [gmx-users] Gromacs and Lammps: energy conservation very different

if it's connected to this. At least if I can rule out a trivial error in my input files, there can be confidence to look deeper. Thanks again for your help. With best regards, James On 6 May 2014 15:09, Mark Abraham mark.j.abra...@gmail.com wrote: On May 6, 2014 4:16 AM, Michael Shirts mrshi

Re: [gmx-users] Gromacs and Lammps: energy conservation very different

regards, James On 6 May 2014 18:42, James jamesresearch...@gmail.com wrote: Dear Michael and Mark, Thanks a lot for your replies. The final 100ps of the 500ps equilibration for Gromacs and Lammps yield the following average energies (all kJ/mol): Total energy per molecule: Gromacs = -37.1

[gmx-users] Polymers

the experience. Thank you for your help. Best regards, James [1] http://www.gromacs.org/Documentation/How-tos/Polymers -- 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

Re: [gmx-users] Polymers

Hello Tsjerk, Thanks, that's very helpful to know. Best regards, James On 5 June 2014 16:10, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi James, The top file is only used to generate the run input file. So it has no real influence on the run in that sense. For the simulation, every molecule

Re: [gmx-users] Subtract structure to a trajectory

Dear Marco, If no-one can suggest a Gromacs tool, it would be easy to output all the co-ordinates of the atoms and then calculate (atom position) - (average structure position) during post-processing. But maybe you know this already. James On 10 July 2014 22:59, Marco Gerolin marco.gero

[gmx-users] Reading double-precision trr file using xdrfile

); (rvec is defined as typedef float rvec[DIM];) Is there any alternative to get them in double precision? Thank you for advice. Best regards, James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] Fatal error in grompp

and updating Octave fixed it. Sincerely, James > -- > > Message: 5 > Date: Sat, 23 Dec 2017 03:43:22 + > From: Mark Abraham <mark.j.abra...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Fatal error from grommp in

Re: [gmx-users] Fatal error from grommp in gromacs 5.0.4

elpful. (That being said, I don't mean to sound too critical -- gromacs is a great tool and I realize there aren't enough resources to make everything perfect.) Sincerely, James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_

Re: [gmx-users] Fatal error from grommp in gromacs 5.0.4

, James On Sat, Dec 23, 2017 at 3:06 PM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, vis

[gmx-users] Correct use of gmx traj -mol ?

be successfully run? Sincerely, James -- 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 https://maillist.sys.kth

[gmx-users] gmx_d energy output at multiple time points?

seems like something that might be built in and I just can't find it in the docs. Thanks! Sincerely, James Ryley -- 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/S

[gmx-users] Getting more detail than is in the documentation

due to my lack of coding skill, not the code). Does anyone know of a reference book, or other sources, that might contain such information? Sincerely, James Ryley -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before pos

Re: [gmx-users] Getting more detail than is in the documentation

obviously you know, just mentioning in case others didn't know this extra info exists). Looks like I have some reading to do! Sincerely, James Ryley -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] Does adding artificial mass cause problems for friction studies?

on this in the literature. Does anyone know about this, or know of relevant studies? Sincerely, James Ryley -- 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

[gmx-users] Question about integrator md-vv and associated documentation

tially reduces total energy drift. I'm just trying to figure out if I can improve it further because it is still a little off, and the drift is always negative (again, going back to whether this is because of the "slightly too small" issue). Sincerely, James Ryley -- Grom

[gmx-users] Do hydrogen bonds innately exist using mdrun?

not "just work," how do you specify them? I could see mimicking them by tuning partial charges on the donor and acceptor atoms to give the correct affinity, but it seems like that still would not be accurate because hbonds are angle dependent, whereas long range non-bonded forces are not. Si

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 178, Issue 37

u have any familiarity with them, do you think any of the reactive force fields are better? (Though even if they are I gather they are about 50X slower, which is essentially intractable for many models) Sincerely, James Ryley, PhD, Patent Agent This communication is confidential and may be subjec

[gmx-users] Restraints not working during minimization

> > Hi, What minimization type are you using? Quasi-Newtonian (L-BFGS) doesn’t > respect restraints; others do. Sincerely, James Ryley > > > -- > > Message: 4 > Date: Thu, 7 Feb 2019 11:03:50 +0530 > From: Ashraya Ravikuma

[gmx-users] Steps to using Drude force field?

eed difference should I expect versus an additive force field? Thanks! Sincerely, James Ryley -- 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

[gmx-users] Getting non-bonded forces from GROMACS

Hi, I am interested in getting only non-bonded force vectors on each atom in an MD run. I know "gmx traj -of" (or "gmx traj -af" -- what's the difference?) will output total forces on atoms, as will "gmx trajectory -of". But, is there a way to only get non-bonded f

Re: [gmx-users] Getting non-bonded forces from GROMACS

s: While I understand that it may not be mathematically rigorous, does decomposing the force field really give meaningless answers (i.e., does not "correlate with something physical")? I could see it not being as accurate as desired, but for it to be useless seems strange to me. Sincerel

[gmx-users] Can GROMACS compute heat flux?

a notion of how much energy is added or removed. Is this possible to do in GROMACS? Sincerely, James Ryley -- 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

[gmx-users] REMD on GPU

from source (without removing of the installed files)? Does it possible to run replica simulations in GPU supported mode ? Thanks for help, James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] Detection of Internal water along MD trajectory

water binding sites. Does SASA calculation which I've seen in vmd could provide me with additional insights? I'd be thankful if you provide me with some Gromacs or VMD tools suitable for such task. Many thanks for help, James -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] Loop refirement using simulated annealing

windows, appropriate implicit solvent models? TFH, James -- 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] Loop refirement using simulated annealing

structures seen in X-ray structures of these proteins have been always absent after such refinement. In this regsaards such refined loops have been looks mostly like random coils. In this case I'd like to test some force-field based SA with the inclusion of implicit solvent models. James 2014-05-28 0

[gmx-users] g_cluster analysis for structure refirement

be performed by g_cluster taking into account that I have gromacs-like trr consisted of my conformers ? On what cluster algoritms and parameters should I pay a lot of attention? Many thanks for suggestion, James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

Re: [gmx-users] g_cluster analysis for structure refirement

cluster of its most representative (not averaged!) structure as the individual pdb? Thanks a lot, James 2014-07-25 12:56 GMT+04:00 Tsjerk Wassenaar tsje...@gmail.com: Hi James, The first part is just conformational clustering, for which you can use g_cluster. The easiest is then to collect

Re: [gmx-users] g_cluster analysis for structure refirement

://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/clustering/ be usefull for such task? James 2014-07-26 11:40 GMT+04:00 Thomas Evangelidis teva...@gmail.com: On 26 July 2014 10:15, James Starlight jmsstarli...@gmail.com wrote: Hi Tsjerk, thanks for suggestions! Some additional

[gmx-users] g_cluster and loops dynamics

me transitions between clusters diagrams ? ( the default xpm file are not vell readable ). Thanks for help, James -- 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

[gmx-users] On the ussing of different equilibration protocols in NPT

(Which act like piston) should produce alot of errors on the stability of the whole system shouldn't it? Does alternatively Parrinello barostat using in Gromacs has completely different preassure coupling method in comparison to langevins piston (in namd) Thanks for suggestions, James -- Gromacs

Re: [gmx-users] On the ussing of different equilibration protocols in NPT

Thank you very much for the suggestion! How do you think are there any drammatic differences between different preassure coupling (barostats) methods implemented not only in Gromacs but in other md packages like amber and namd? What barostat will be better for memrbane protein simulation ? James

[gmx-users] How to calculate protein-surface interaction energy

? secondly, Is there any way to average the energy over the last 10ns of MD trajectory in Gromacs?? Cheers James -- 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

[gmx-users] Fwd: How to calculate protein-surface interaction energy

? secondly, Is there any way to average the energy over the last 10ns of MD trajectory in Gromacs?? Cheers James -- 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

[gmx-users] Fwd: How to calculate protein-surface interaction energy

wrong? secondly, Is there any way to average the energy over the last 10ns of MD trajectory in Gromacs?? Cheers James -- 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

Re: [gmx-users] How to calculate protein-surface interaction energy

Hi Justin, Thanks, the .mdp is the same as your tutorial for lysozyme, Can you explain a bit more what to do? if I want to have total energy= vdw and electrostatic? Cheers James On Fri, Oct 17, 2014 at 12:51 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/16/14 5:46 AM, James Lord wrote

Re: [gmx-users] How to calculate protein-surface interaction energy

an example of the command with appropriate input output etc. Cheers James On Fri, Oct 17, 2014 at 3:49 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/16/14 10:47 AM, James Lord wrote: Hi Justin, Thanks, the .mdp is the same as your tutorial for lysozyme, Can you explain a bit more what to do? if I

Re: [gmx-users] How to calculate protein-surface interaction energy

file energygrps= protein surface saved it and grompp -f md.mdp -c mdw.gro -t mdw.cpt -p toplgy.top -o mdnew mdrun -s mdnew.tpr -rerun mdw.xtc g_energy -f mdnew.edr -o energy.xvg Thanks James On Sat, Oct 18, 2014 at 8:52 AM, Diogo Martins de Sá sadi...@mol.bio.br wrote: open your .mdp

Re: [gmx-users] How to calculate protein-surface interaction energy

is a not charged (polyethylene)?? I'd expect zero energy at beginning and upon touching the surface negative value??? any comments? Sorry this has nothing to do with Gromacs. Cheers James On Sat, Oct 18, 2014 at 11:48 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/18/14 6:45 AM, James Lord wrote: Dear

Re: [gmx-users] How to calculate protein-surface interaction energy

atom Cheers James On Sun, Oct 19, 2014 at 2:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/18/14 8:51 AM, James Lord wrote: Hi Justin, Thanks for the prompt answer. I selected LJ-(SR) but I am getting a positive fluctuating line over the simulation time. Looking at the vmd movie I can

Re: [gmx-users] How to calculate protein-surface interaction energy

You are right it is the name of molecule type in .top, and thus no error upon executing grompp, so index group is constructed correctly right??? rvdw=1 nm so should be fine. and for the last part I agree. Cheers James On Sun, Oct 19, 2014 at 2:34 AM, Justin Lemkul jalem...@vt.edu wrote: On 10

Re: [gmx-users] How to calculate protein-surface interaction energy

to the mailing list. Is that fine with you? Cheers James On Sun, Oct 19, 2014 at 4:26 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/18/14 9:55 AM, James Lord wrote: You are right it is the name of molecule type in .top, and thus no error upon executing grompp, so index group is constructed correctly

Re: [gmx-users] How to calculate protein-surface interaction energy

Hi Diogo, Yes that is what I have at the end of top file. ps: Sorry Justin I just saw your previous email. Cheers James On Sun, Oct 19, 2014 at 2:13 PM, Diogo Martins de Sá sadi...@mol.bio.br wrote: At the end of your topology file, what molecules do you have written down? You should have

Re: [gmx-users] How to calculate protein-surface interaction energy

Hi Justin, Here is the uploaded files on 4share. http://www.4shared.com/folder/9CgRBgqp/_online.html Cheers James On Sun, Oct 19, 2014 at 2:23 PM, James Lord jjamesgreen...@gmail.com wrote: Hi Diogo, Yes that is what I have at the end of top file. ps: Sorry Justin I just saw your previous

Re: [gmx-users] How to calculate protein-surface interaction energy

you described before as being problematic. Cheers James -Justin On Sun, Oct 19, 2014 at 4:18 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/18/14 10:41 PM, James Lord wrote: Hi Justin, Here is the uploaded files on 4share. http://www.4shared.com/folder/9CgRBgqp/_online.html Well, I tried

Re: [gmx-users] How to calculate protein-surface interaction energy

Hi Justin, Would you please tell me from the files I sent you which of them you checked and how you got to the conclusion that (I mean which command ) This system behaves correctly - there is a zero interaction energy (both Coulomb and LJ) at t=0, so it is fine. Thanks James On Mon, Oct 20, 2014

[gmx-users] How to obtaine different protein orientations in a biphasic system

periodic boundary condition in XYZ, Am I really obtaining different orientations? any comments is appreciated Cheers James -- 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

[gmx-users] merging chains in gromos43a1p

prefer to number them sequentially. The sequential numbering helps in indexing for simulated annealing because it is easy to choose the amino acids that I need to heat and cool. Thank you Jayant James -- Jayasundar Jayant James http://www.chick.com/reading/tracts/0076/0076_01.asp -- Gromacs Users

Re: [gmx-users] merging chains in gromos43a1p

the latest version of GMX would solve the problem? Thanks James --- Program pdb2gmx, VERSION 4.5.4 Source code file: statutil.c, line: 819 Invalid command line argument: -merge For more information and tips for troubleshooting, please check the GROMACS

[gmx-users] Protein distance with respect to box walls

Dear Users, I have a protein in a box and was wondering to know how to figure out the protein distance to the box walls? I can see the box dimensions at the end of .gro file but how to know what is (x,y,z) of protein in the box?? any comments? Cheers James -- Gromacs Users mailing list * Please

[gmx-users] g_mindist

?? Cheers James -- 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 https://maillist.sys.kth.se/mailman/listinfo

[gmx-users] Illegal instruction flag raised in GMX 5.0.4

appreciate any suggestions Thank you Jayant James ERROR MESSAGE -- GROMACS: gmx editconf, VERSION 5.0.4 Executable: /share/apps/gromacs/5.0.4/bin/gmx Library dir: /share/apps/gromacs/5.0.4/share/gromacs/top Command line: editconf -h Illegal instruction

[gmx-users] PCA projections using g_anaeig

although 1-3 modes has been calculated. How it would be possible to make the same graph using 1 and 3rd components instead? Thanks for help, James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post

Re: [gmx-users] PCA projections using g_anaeig

Thx, Tsjerk! So normally gromacs make 2D projections exactly only on 1 and 2 components (even if 100 modes have been calculated for instance) doest it? 2015-01-28 16:13 GMT+01:00 Tsjerk Wassenaar tsje...@gmail.com: Hi James, If you have the 1D projections as 1.xvg and 3.xvg: paste 1.xvg 3

[gmx-users] Validation suite for force fields for Proteins, RNA, DNA and Lipids?

Spoel , J. Chem. Theory Comput., 2012, 8 (1), pp 61-74 Can anyone point me to a similar analysis of force fields for Proteins, RNA, DNA and Lipids? Thanks. Jim James Kress Ph.D., President The KressWorks Foundation C An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

[gmx-users] Distance of residue’s centre of mass to a surface (COM)

distance are written to two separate output files. Cheers James -- 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

Re: [gmx-users] Questions regarding usage of the covariance analysis

just forgot to ask 3) how it will be possible to mark on the projections as well as on the free energy landscapes points corresponded to the initial and final conformations along the trajectory? 2015-02-28 19:21 GMT+01:00 James Starlight jmsstarli...@gmail.com: Dear Gromacs users! Here I'd

[gmx-users] Questions regarding usage of the covariance analysis

time. 2) Is it possible to improve quality (resolution) of the colored free energy diagrams made by g_sham –f 2dproj_1_2.xvg –ls gibbs.xpm -notime xpm2ps –f gibbs.xpm –o gibbs.eps –rainbow red Thanks for help! James -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] On the collective dynamics in terms of NMA and PCA

possible states along its pathway. Does it correct? In any case It's not quite understand for me why the directions of the first PCs (most collective dynamics) should be at the same time more softest (less-energy consuming pathways). Thanks for suggestions again! James 2015-02-24 11:42 GMT+01:00

Re: [gmx-users] Distance of residue’s centre of mass to a surface (COM)

anything? Cheers James On Sat, Mar 28, 2015 at 1:17 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/27/15 8:03 AM, James Lord wrote: Dear users, If I want to calculate distance of each residue's COM of a protein to a surface is g_mindist going to be my friend? It is documented

Re: [gmx-users] Extraction of the pdb data from the g_shame diagrams

and what the most trivial way to find correspondence of the line in the data file to what I actually see on the its graph (projection) ? Sorry I'm not an expert of xmgrace so it might seems for you trivial :) Regards, James 2015-04-17 20:18 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 4/17

Re: [gmx-users] trjconv for cutting the trajectory in small subtrajectories

Hi Mahboobeh, I recommend checking the created trajectories with gmx check. Cheers James On Sun, Apr 26, 2015 at 12:39 AM, Ming Tang m21.t...@qut.edu.au wrote: Hi，-e is end frame， -b is the start one. Sent from my Huawei Mobile Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi GMx

[gmx-users] Justin biphasic tutorial with controlled adsoption of protein

is the best way to do it? any suggestion? here is the mdp https://drive.google.com/open?id=0B0YMTXH1gmQsZ1ljOUZROWNGM3Mauthuser=0 cheers James -- 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

Re: [gmx-users] Justin biphasic tutorial with controlled adsoption of protein

not get what to do for position restrains, appreciate if you can elaborate further on it? Thanks for your final point re solvent/ions separate coupling. https://drive.google.com/file/d/0B0YMTXH1gmQsYmQzRXUtN1ZENmc/view?usp=sharing Cheers James On Sun, May 3, 2015 at 4:23 AM, Justin Lemkul jalem

[gmx-users] Area/enegy at liquid/liquid interface

is much appreciated. Cheers James -- 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 https://maillist.sys.kth.se

[gmx-users] gromacs-5.0.4 installation problem

occurred! See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeOutput.log. See also /home/james/gromacs-5.0.4/build/CMakeFiles/CMakeError.log. After this I did sudo apt-get install nvidia-cuda-toolkit but still i am getting the same message Any comments? Cheers James -- Gromacs Users mailing

Re: [gmx-users] gromacs-5.0.4 installation problem

software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. So are you guys saying that a new installation might be better than messing around with this? Cheers James On Thu, May 7, 2015 at 7:21 PM, Szilárd Páll

Re: [gmx-users] gromacs-5.0.4 installation problem

YAY :-) it is working, Do not know what was wrong but apparently something was seriously messed up with cmake and compilers, removed cmake and gcc gcc++ complier and gromacs, re-doing solved the problem. *sudo apt-get update -y* *sudo apt-get update**sudo apt-get install cmake* Cheers James

[gmx-users] modelling/adding missing residues in case of Fatal error: Incomplete ring in HIS3

them? Again somewhere else Justin is saying “add the missing atoms with emacs (or another text editor). Then minimize” . May I ask someone to walk me through these steps? Cheers James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

Re: [gmx-users] modelling/adding missing residues in case of Fatal error: Incomplete ring in HIS3

Hi Justin, I opened up the strucutre in Swissviewr. Then how can I have a pdb with missing parts added? Cheers James On Tuesday, May 5, 2015, Justin Lemkul jalem...@vt.edu wrote: On 5/5/15 4:32 AM, James Lord wrote: Dear gmx users, pdb2gmx is complaining about Incomplete ring in HIS3

Re: [gmx-users] modelling/adding missing residues in case of Fatal error: Incomplete ring in HIS3

can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program pdb2gmx, VERSION -4.5.4 Source code file: /home/James/gromacs-4.5.4/src/kernel/resall.c, line: 642 Fatal error: Residue 'ACT

Re: [gmx-users] modelling/adding missing residues in case of Fatal error: Incomplete ring in HIS3

Thanks Justin. On Wed, May 13, 2015 at 11:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/13/15 6:16 AM, James Lord wrote: Many thanks Justin, I created a new .pdb file with SwissPDBViewr but again executing pbd2gmx is giving the following warning and error Warning: Starting residue

[gmx-users] total charge (qtot)

Cheers James -- 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 https://maillist.sys.kth.se

Re: [gmx-users] total charge (qtot)

I can see that I have two chains but can I simply say the total charge is -7 e? Cheers James On Thu, May 14, 2015 at 1:04 AM, James Lord jjamesgreen...@gmail.com wrote: Dear gmx users, I am trying to repeat Justin's Lysozyme tutorial for 1HFX.pdb, https://drive.google.com/file/d

Re: [gmx-users] genion error sol not continuous

/file/d/0B0YMTXH1gmQsMjlMTlNPeWJqdkk/view?usp=sharing Thanks James On Fri, May 15, 2015 at 4:36 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/14/15 1:25 AM, James Lord wrote: Hi all, I am trying to neutralize this system (1HFX.gro) and genion is complaining about solvent not being continuous

[gmx-users] Extraction of the pdb data from the g_shame diagrams

possible to extract pdb of the protein corresponded to those short-lived intermediates just form the projection data avoiding of the GUI visualization of the trajectory? Thanks for help! James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Forced adsoprtion and desorption of a protein on a surface

Thanks heaps mastermind Justin. James On Thursday, April 9, 2015, Justin Lemkul jalem...@vt.edu wrote: On 4/9/15 2:45 AM, James Lord wrote: Dear Users, I am wondering if anyone can help me out with forced adsorption/ desorption of a protein on surface. I am aware of pulling code

[gmx-users] Forced adsoprtion and desorption of a protein on a surface

the protein (center of mass) onto /or from a surface at specific time intervals during the simulation . Appreciate any comments. Cheers James -- 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

[gmx-users] Biphasic Systems for BSA

/d/0B0YMTXH1gmQsdGd2Z2xtVENzZkk/view?usp=sharing Cheers James -- 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

Re: [gmx-users] energy minimization error

Hi Justin For now I used *mdrun -nt 1* * and got rid of this error so hopefully the simulation wont crash. * *Cheers* *James* On Sat, Jun 27, 2015 at 11:19 AM, James Lord jjamesgreen...@gmail.com wrote: Hi Justin, I have asked this before, but this time I started up from scratch

Re: [gmx-users] energy minimization error

://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing Cheers James On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/16/15 11:35 PM, James Lord wrote: Hi Justin Thanks for this. Can you tell me which step(s) this bond length is defined What should I

Re: [gmx-users] Biphasic Systems for BSA

Hi Justin Tsjerk, Thanks for the info, Tsjerk: I was looking for the monomer but could not find monomer structure on protein data bank. Cheers James On Sun, Jun 28, 2015 at 6:50 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi, Actually no, you may be better off with a hexagonal prism

Re: [gmx-users] Biphasic Systems for BSA

/27/15 7:46 PM, James Lord wrote: Hi Justin Tsjerk, Thanks for the info, Tsjerk: I was looking for the monomer but could not find monomer structure on protein data bank. Because it crystallizes as a dimer. The state in the crystal is not necessarily what one finds in solution. Just pull

Re: [gmx-users] Biphasic Systems for BSA

Thanks heaps Justin On Sun, Jun 28, 2015 at 1:58 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/27/15 9:48 PM, James Lord wrote: Hi Justin, Thanks for your email. Would you please tell me how I can do this? Sorry to bother you. below is the PBD I generated with Swiss-PdbViewr. https

[gmx-users] GPU gromacs

compatible controller: NVIDIA Corporation GF108M [GeForce GT 635M] (rev a1) any thoughts is greatly appreciated. Cheers James -- 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

[gmx-users] Fwd: Question about editconf -noc flag

, using editconf -f OCT_npt.gro -oOCT_newbox.gro -box 6.47271 6.47271 16 -noc https://drive.google.com/open?id=0B0YMTXH1gmQsT1M3dzBNNTJrT28 I used the last flag to put the oil at the ends of box but it is not doing for one end? any thoughts? Cheers James -- Gromacs Users mailing list * Please

[gmx-users] editconf -density

-density 824 But it changes the x,y,z to adjust the density. Is it possible to ask editconf to do this only by changing for example z? Cheers James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post

Re: [gmx-users] Gromos 53a6, .mdp parameters for reaction field

Hi Mohsen, I am struggling with the same problem would you mind if I ask you to send me your .mdp file ? Cheers James On Tue, Aug 11, 2015 at 4:00 AM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: As an update, After reading the suggested links I tried two .mdp files which were

Re: [gmx-users] Gromacs Path

Hi Vikas, typing mdrun or which mdrun in your terminal will tell you where it is installed. Cheers James On Monday, July 27, 2015, Live King vikasdubey1...@gmail.com wrote: Hi Everyone, I installed Gromacs-4.6.5 using the command sudo apt-get install gromacs, then what is path of my Gromacs

Re: [gmx-users] Question about biphasic tutorial

Hi Justin, Welcome back. Thanks I solved it the other day. I got the coordinate and topology. Cheers James On Monday, July 27, 2015, Justin Lemkul jalem...@vt.edu wrote: On 7/24/15 4:16 AM, James Lord wrote: Hi all, I want to make the the hydrophobic layer Justin has made but only have one

[gmx-users] Question about biphasic tutorial

://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg,. any comments? Cheers James -- 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

[gmx-users] Fwd: itp file not found

%2f%2fwww.gromacs.org%2fAbout_Gromacs%2fRelease_Notes%2fVersions_4.6.x Program grompp, VERSION 4.6.3 Source code file: /home/James/gromacs-4.6.3/src/gmxlib/gmxcpp.c, line: 293 Fatal error: Topology include file ffG54a7.itp not found For more information and tips for troubleshooting, please check

[gmx-users] itp file not found

%2f%2fwww.gromacs.org%2fAbout_Gromacs%2fRelease_Notes%2fVersions_4.6.x Program grompp, VERSION 4.6.3 Source code file: /home/James/gromacs-4.6.3/src/gmxlib/gmxcpp.c, line: 293 Fatal error: Topology include file ffG54a7.itp not found For more information and tips for troubleshooting, please check

[gmx-users] Fwd: itp file not found

-JZkbI7m1r4rIAoHfY4Juci2q9ENk7mUf5LSCGgAdAB0AHAAOgAvAC8AdwB3AHcALgBnAHIAbwBtAGEAYwBzAC4AbwByAGcALwBBAGIAbwB1AHQAXwBHAHIAbwBtAGEAYwBzAC8AUgBlAGwAZQBhAHMAZQBfAE4AbwB0AGUAcwAvAFYAZQByAHMAaQBvAG4AcwBfADQALgA2AC4AeAA.URL=http%3a%2f%2fwww.gromacs.org%2fAbout_Gromacs%2fRelease_Notes%2fVersions_4.6.x Program grompp, VERSION 4.6.3 Source code file: /home/James/gromacs-4.6.3/src/gmxlib/gmxcpp.c, line: 293 Fatal error: Topology

[gmx-users] Fwd: hydrogen bonds

1568 8234 1567 1568 8238 1567 1568 8240 1567 1568 8259 1567 1568 8261 1567 1568 8675 1567 1568 8676 1567 1568 8679 1567 1568 8681 1567 1568 8700 1567 1568 8702 1591 1592 5111 Cheers, James -- Gromacs Users mailing list

[gmx-users] Question regarding box size

optimum size in each direction so that the protein does not see its periodic image. Appreciate any specific thoughts on my system and the box size I have got now. https://drive.google.com/file/d/0B0YMTXH1gmQsdFVKWkdPLURCUVk/view?usp=sharing Cheers James -- Gromacs Users mailing list * Please search

Re: [gmx-users] Question regarding box size

Thanks Justin and Victor On Sat, Jul 11, 2015 at 9:12 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/10/15 1:35 AM, James Lord wrote: Hi all, I have a system with 300k atoms, but computationally it is expensive for me doing simulation with such a big system, Is it possible to reduce

Re: [gmx-users] GPU gromacs

Thanks Slizard. I need to get this simulation done in a week but does not have the right facilities. Is there anyone in the group with some high end GPU cards that can help me get this running. Cheers James On Tuesday, July 7, 2015, Szilárd Páll pall.szil...@gmail.com wrote: Of course you can

[gmx-users] biphasic simulation and surface-surface tension calculation

surface-surface tension g_energy -f energy.edr -s md.tpr -o surften.xvg selecting #Surf*SurfTen when asked Cheers James -- 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

Re: [gmx-users] force fields selection

Hi Antonio, Thanks for further information and the paper. Cheers James On Thu, Sep 24, 2015 at 3:30 AM, Antonio Baptista <bapti...@itqb.unl.pt> wrote: > On Tue, 22 Sep 2015, Justin Lemkul wrote: > > >> >> On 9/21/15 10:22 PM, James Lord wrote: >> >>

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