Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

Maybe you should modify your .tpr file manually according to what you added in the previous sections! On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: dear timo Please send me further details. I'm not a professional. Thanks and regards On Thursday,

Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

Oh, I am sorry, I made a big mistake! :) Best Regards On Thu, Nov 28, 2013 at 6:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote: Maybe you should modify your .tpr file manually according to what you added in the previous sections! Manually

Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

Dear Justin I meant modifying .top file after adding some ions and water molecules which could be equivalent to -p option as you mentioned. What do you think about this? Please let me know On Thu, Nov 28, 2013 at 6:37 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Oh, I am

[gmx-users] More suitable force field and water model

Dear Gromacs Users, I have read some articles about the more appropriate combination of force field and water model for different simulations of interest. It is confusing and too difficult to decide which combination is the best one. Besides according to articles I read, I am in doubt now and not

Re: [gmx-users] More suitable force field and water model

Dear Justin, On Thu, Jun 19, 2014 at 3:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/19/14, 5:59 AM, Mohsen Ramezanpour wrote: Dear Gromacs Users, I have read some articles about the more appropriate combination of force field and water model for different simulations of interest

Re: [gmx-users] Fwd: Umbrella sampling Tutorial Fatal Error

Hi, Did you check the parameters in .mdp file for pulling simulation?! I think you have to define this pulling group in .mdp file that you use in grompp. On Fri, Feb 27, 2015 at 7:16 PM, Nima Soltani nima@gmail.com wrote: Excuse me that I forgot to attach the complete Error page:

Re: [gmx-users] RMSD between two groups

Hi, How about using g_dist and using an index file?! Cheers Mohsen On Mon, Mar 23, 2015 at 6:50 PM, leila salimi leilasal...@gmail.com wrote: Dear all, I have a question regarding to analyse the trajectory that I have. I am studying the interaction of peptide at interfaces, e.g Oxygen of

[gmx-users] making bilayers including a lipid-like molecule

Dear Gromacs users, I was wondering how can I make initial structures for bilayers, micells and liposomes composed of different lipids including some lipid-like molecules. I am interested in different mixing ratios in two leaflets in bilayer and liposome cases. I have the coordinate and topology

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

the nstlist to 1, this also works for my system. Thanks for your comments. Cheers Mohsen On Tue, Jul 21, 2015 at 4:44 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: I looked at the first link, it was a useful discussion. Now, I am trying suggestions with rlist/r(columb/vdw)=(1.4/1.4

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

Dear Gromacs users, I am interested in simulation of lipid bilayers with Gromos96 53a6. As I understood this force field has been parametrized with reaction field instead of pme. Based on literatures, I have the following .mdp parameters: But I am not sure of those as my system has lots of LINCS

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

contraint often results in different problems. You will have to play with the relevant parameters, like lincs_order and allowable deviation. On Tue, Jul 21, 2015 at 2:28 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Gromacs users, I am interested

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

and allowable deviation. On Tue, Jul 21, 2015 at 2:28 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Gromacs users, I am interested in simulation of lipid bilayers with Gromos96 53a6. As I understood this force field has been parametrized with reaction field instead

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

with gromacs 3-3-3 (imagine when it was). Professor Vitaly V. Chaban On Tue, Jul 21, 2015 at 4:49 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Hi Chaban, Me too, but I do not know why starting with the same initial structures and also starting from equilibrated

Re: [gmx-users] G53A6, non-symmetric selection metrix

.org_gmx-users-boun...@maillist.sys.kth.se [ > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mohsen > Ramezanpour [ramezanpour.moh...@gmail.com] > Sent: 10 December 2015 23:42 > To: Discussion list for GROMACS users > Subject: [gmx-users] G53A6, non-symmetric selection m

[gmx-users] G53A6, non-symmetric selection metrix

Dear All, Reading the parameters for Gromos 53A6 ff ( article by Oostenbrink *et al. Journal of computational chemistry* 25.13 (2004): 1656-1676.), I got confused about van der waals interactions between non-bonded atoms. for two atom types, we use combination rules to get (Cij 6) and (Cij 12),

Re: [gmx-users] making topology file manually

D 2) check for the correct numbers of assigned lines based on information in force field files (ffbonded, ffnonbonded) and of course validating the simulation results Best, Mohsen On Tue, Jun 7, 2016 at 6:33 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/7/16 12:49 PM,

[gmx-users] making topology file manually

Dear All, I am trying to insert a 5-atom ring composed of carbon and non-carbon atoms in the middle of my small molecule. Reading literature, I have got confused a bit. Especially about the "pairs", "exclusions", and "improper dihedrals" sections in topology file. Is anyone aware of any

[gmx-users] Ring planarity

Dear Gromacs users, I am working on a Protein-drug interaction problem. The small molecule has a cytosine ring. Based on QM calculations and PDB database, The structure for this ring should be planar. However, doing simulations the the ring is not completely planar . Besides, the NH2 group on

[gmx-users] Lipid parameterization

Dear Gromacs users, I am trying to parameterize a lipid molecule with a weird headgroup :-) in Charmm36 force field for doing simulation in GROMACS. Reading through literature, I found that Swissparam, and Paramchem.org are two useful tools to make the topology files automatically. However, both

Re: [gmx-users] Lipid parameterization

> > -Justin > > > Chris. >> >> ____ From: >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mohsen >> Ramezanpour <ramezanpour.moh...@gmail.com&g

[gmx-users] CTP .gro and .itp file

Dear All, I am interested in doing MD simulation on protein and CTP molecule, preferably in amber99sb-ildn ff in Gromacs. Well, I think we can also use GAFF for CTP in combination with amber99-sb-ildn for protein. Please correct me if I am wrong. There are parameter files for ATP and GTP in

Re: [gmx-users] periodic boundary conditions

deformation. However the 6-around-1 can e.g. deform each > wall of the central hexagonal cell independently. Whether any of these make > a "correct" model depends what you're trying to model. > > Mark > > On Wed, Jul 13, 2016 at 2:41 AM Mohsen Ramezanpour < >

Re: [gmx-users] periodic boundary conditions

Any other comment on this? :-) On Wed, Jul 13, 2016 at 9:50 AM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Mark, > > Thanks for your reply. > > The 6 around 1 setup is also periodic. > > I understand this. However, we can argue the same for

Re: [gmx-users] Correct .mdp file for Amber99SB-ILDN ff implementation in Gromacs

areful, systematic study of cutoff effects (which is probably a paper > or two in and of itself), then that user should follow the people who > actually made the force field. A model is only valid under the conditions > which are known to be valid :) > > -Justin > > > Ho

[gmx-users] Restraints/constraints for keeping a helix as helical

Dear Gromacs users, In my simulation, I am interested to keep specific part of an alpha-helix (e.g. residues 10-15) as helical through whole production run. This has been discussed a few time in mailing list but I could not get my answers. Reading through Gromacs manual, and mailing list, I found

[gmx-users] periodic boundary conditions

Dear gromacs-users, Doing simulations on lipid HII phase, I came to a question which I could not get happy with my answer. I appreciate your opinion in advance: Imagine you have a cylinder made of lipids with waters only inside the cylinder, which is long enough and can be run for enough time so

[gmx-users] Correct .mdp file for Amber99SB-ILDN ff implementation in Gromacs

Dear Gromacs-users, I am interested in simulation of protein-ligand system. To do so, I have chosen the amber99sb-ildn force field. Reading through the original paper on this force filed by D.E.Shaw group (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/) I have made the following

[gmx-users] Any script available?

Dear gromacs users, I was wondering if there is any script available for making 1) atomistic inverted hexagonal phase? e.g. to make HII phase composed of three new lipids with non-common head groups. 2) for replacing the headgroup of lipids in an equilibrated system? e.g. to replace the

[gmx-users] Fwd: Restraints/constraints for keeping a helix as helical

Dear All, I was wondering if you have any comment or suggestion on this post. Any comment is appreciated in advance. Best, Mohsen -- Forwarded message -- From: Mohsen Ramezanpour <ramezanpour.moh...@gmail.com> Date: Wed, Aug 10, 2016 at 7:17 PM Subject: Restraints/const

[gmx-users] Dihedral Population Analysis -Index file

Dear Gromacs users, I have a trajectory file which I wish to do a dihedral analysis for specific dihedral. Based on what I understood from mailing list and manual, I made an index.ndx manually for the dihedral of interest in the molecule. Usually, when we make an index file, say for atom P in

Re: [gmx-users] dihedral MM scan

, 2017 at 7:48 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/19/17 9:40 PM, Mohsen Ramezanpour wrote: > >> Thanks Justin, >> >> I did the scan for the whole range from -180 to 180 in 10 intervals. >> I used emtol = 50, and restrain forc

Re: [gmx-users] Dihedral Population Analysis -Index file

aham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Tue, Jan 24, 2017 at 12:35 AM Mohsen Ramezanpour < > ramezanpour.moh...@gmail.com> wrote: > > > Dear Gromacs users, > > > > I have a trajectory file which I wish to do a dihedral analysis for > >

Re: [gmx-users] dihedral MM scan

t 10:14 PM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Justin, > > I did a dihedral population analysis in both bilayer and HII phase. > Interestingly, the population analysis is consistent with the QM profile > from GAAMP. (i.e. I see more population in deep

Re: [gmx-users] Dihedral Population Analysis -Index file

he > way > http://manual.gromacs.org/documentation/5.1/onlinehelp/ > selections.html#permuting-selections-permute > describes. You want 4 2 1 3 > > Mark > > On Tue, 24 Jan 2017 21:46 Mohsen Ramezanpour <ramezanpour.moh...@gmail.com > > > wrote: > > > Thanks Mark.

Re: [gmx-users] dihedral MM scan

to see what is the problem. Based on these analysis I expect to get quite good MM PES profiles. Cheers Mohsen On Tue, Jan 24, 2017 at 1:48 PM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Justin, > > Sorry, I am just doing some dihedral population analysis to

[gmx-users] Order Parameter for HII phase

Dear Gromacs users, I am interested in calculation of order parameter of lipids in a HII phase. I am not sure about the correct command to use. Which one of the following should I use to be able to compare my data with deutirated NMR experiments? 1) gmx order -f md.xtc -n index.ndx -s

Re: [gmx-users] Order Parameter for HII phase

es with the SCD given by g_order > (I once did that, just to be sure). > > Good luck! :) > > Best, > Antonio > > > > On Thu, 23 Feb 2017, Justin Lemkul wrote: > > >> >> On 2/23/17 1:25 PM, Mohsen Ramezanpour wrote: >> >>> And I agree with

Re: [gmx-users] Order Parameter for HII phase

? Cheers Mohsen On Thu, Feb 23, 2017 at 10:06 AM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Justin, Piggot, > > Thanks for your replies. > I agree with that. The problem is that the situation is straightforward > for bilayers as bilayers are usually in spec

Re: [gmx-users] Order Parameter for HII phase

2017 12:16 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Order Parameter for HII phase > > On 2/22/17 9:51 PM, Mohsen Ramezanpour wrote: > > Dear Gromacs users, > > > > Unfortunately, I did not get any reply on this post. > > > > I was wond

[gmx-users] Fwd: Order Parameter for HII phase

Hi Everyone, I was wondering if someone has any suggestion on the following post, please? Cheers Mohsen -- Forwarded message -- From: Mohsen Ramezanpour <ramezanpour.moh...@gmail.com> Date: Thu, Feb 16, 2017 at 3:13 PM Subject: Order Parameter for HII phase To: Discussio

Re: [gmx-users] Order Parameter for HII phase

on with 2 H NMR experiments" by Vermeer et al. (2007) Thanks in advance for your comments Mohsen On Sun, Feb 19, 2017 at 10:18 AM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Everyone, > > I was wondering if someone has any suggestion on the following

Re: [gmx-users] Question regarding equilibration of the system

Hi Ali, There are several parameters to check. It is, however, highly dependent to the system. Please describe your system, is it a protein-ligand system, a lipid bilayer, ... ? For lipid bilayers, the box size, and consequently, the are per lipid is a good one to check for. Cheers On Thu, Feb

[gmx-users] dihedral MM scan

Dear Gromacs users, I want to do a MM scan on a dihedral and compare with the available QM profile using Gromacs 5.1.3 I used the following (updated compared to my last email on parameters) em.mdp and md.mdp files for relaxation and zero-step md, respectively. *em.mdp:* define

Re: [gmx-users] MM dihedral scanning

And oh, none of the Kenno's web pages for tutorial and software is working at the moment. On Tue, Jan 17, 2017 at 8:37 PM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Gromacs users, > > I want to follow recommended procedure (by Justin) for MM scanning of > r

Re: [gmx-users] MM dihedral scanning

wrote: > > > On 1/13/17 3:26 PM, Mohsen Ramezanpour wrote: > >> Thanks. interesting! >> So, for now, lets focus on one of those dihedrals which has another >> equivalent. >> If I do PES on a rotatable bond in one ethyl, the other equivalent >> rotatabl

Re: [gmx-users] MM dihedral scanning

On Wed, Jan 18, 2017 at 10:35 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/17/17 10:37 PM, Mohsen Ramezanpour wrote: > >> Hi Gromacs users, >> >> I want to follow recommended procedure (by Justin) for MM scanning of >> rotatable dihedrals and do

Re: [gmx-users] MM dihedral scanning

f version 5) Cheers On Tue, Jan 17, 2017 at 8:39 PM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > And oh, none of the Kenno's web pages for tutorial and software is working > at the moment. > > On Tue, Jan 17, 2017 at 8:37 PM, Mohsen Ramezanpour < > rame

Re: [gmx-users] dihedral MM scan

in advance. Cheers Mohsen On Wed, Jan 18, 2017 at 7:55 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/18/17 9:51 PM, Mohsen Ramezanpour wrote: > >> Dear Gromacs users, >> >> I want to do a MM scan on a dihedral and compare with the available QM >>

[gmx-users] Gromac4.6.7 installation problem

Dear Gromacs users, I am trying to install gromacs 4.6.7 on Ubuntu 16.04. Unfortunately, I get an Error which I do not know how to solve it. After mkdir build cd build *I use:* cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON

[gmx-users] anisotropic pressure coupling

Dear gromacs users, If we are interested in deformation in simulation box shape (*both angles and lengths*) during simulation for a lipid system, like what has been done in this article (fig 1, fig 2, and fig 3): "Phase behavior of a phospholipid/fatty acid/water mixture studied in atomic

[gmx-users] high pressure and temperatures: force field parameters

Dear gromacs users, Force field parameters are not usually parametrized for high pressures and temperatures. say for P=500 bar! or for T=500 K Although we can do simulations, but we cannot trust on the results. Is there any maximum (or range ) defined somewhere in the literature (which I am

[gmx-users] position restrain on a curved surface

Dear gromacs users, I was wondering what would be a good strategy to force atoms to move on an arbitrary curved surface? An example could be forcing lipid molecules to freely move on x-y plane while their z coordinate is fixed. This is easy because curvature is zero here. How about the curved

Re: [gmx-users] high pressure and temperatures: force field parameters

> Micholas Dean Smith, PhD. > Post-doctoral Research Associate > University of Tennessee/Oak Ridge National Laboratory > Center for Molecular Biophysics > > ________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@mail

Re: [gmx-users] anisotropic pressure coupling

Hi Everyone, Please let me know your opinion on this question. Thanks in advance Mohsen On Wed, Sep 7, 2016 at 5:35 PM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Dear gromacs users, > > If we are interested in deformation in simulation box shape (*both angle

Re: [gmx-users] anisotropic pressure coupling

make sure you read the documentation of the respective .mdp options. > > Mark > > On Mon, Sep 12, 2016 at 5:54 PM Mohsen Ramezanpour < > ramezanpour.moh...@gmail.com> wrote: > > > Hi Everyone, > > > > Please let me know your opinion on this question. Thanks in advance &

Re: [gmx-users] Fwd: self-assembly and box size

On Mon, Nov 14, 2016 at 7:27 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/14/16 9:04 PM, Mohsen Ramezanpour wrote: > >> Thanks Justin for your comments. >> >> Comments interspersed. >> >> On Mon, Nov 14, 2016 at 6:47 PM, Justin Lemkul <

Re: [gmx-users] Fwd: self-assembly and box size

Thanks Justin for your comments. Comments interspersed. On Mon, Nov 14, 2016 at 6:47 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/14/16 5:11 PM, Mohsen Ramezanpour wrote: > >> Dear Gromacs users, >> >> I have made an initial system with a

[gmx-users] Melting temperature for the lipid bilayer

Dear gromacs users, Running simulation on a lipid bilayer made by Charmm-GUI, there is about 24 degrees difference between the reported temperature in Avanti and what I see in my simulations for getting a liquid disordered (L_disorder) bilayer. I am using all-atom Charmm36 FF for simulations. I

Re: [gmx-users] Melting temperature for the lipid bilayer

It is worth mentioning that with Gromos53a7, the model was made by merging head group and tails, I got T= 353 K for the right phase. On Tue, Nov 22, 2016 at 2:37 PM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Justin, > > Comments interspersed. > > On Tue,

Re: [gmx-users] Melting temperature for the lipid bilayer

Hi Justin, Comments interspersed. On Tue, Nov 22, 2016 at 1:18 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/21/16 3:28 PM, Mohsen Ramezanpour wrote: > >> Dear gromacs users, >> >> Running simulation on a lipid bilayer made by Charmm-GUI, there

Re: [gmx-users] Melting temperature for the lipid bilayer

__ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mohsen > Ramezanpour <ramezanpour.moh...@gmail.com> > Sent: 22 November 2016 16:40:08 > To: Discussion list for GROMACS users > Subjec

Re: [gmx-users] question

Hi, I assume you meant some water molecules was located in the middle of bilayer while adding solvent, right? If yes: Please have a look at this article for solvation part: Kandt, Christian, Walter L. Ash, and D. Peter Tieleman. "Setting up and running molecular dynamics simulations of membrane

[gmx-users] molecule parameterization in charmm36 using GAAMP server

Dear Gromacs users, I used GAAMP server to get the parameters for a small molecule (this is part of a larger molecule). This server optimizes the charges and all the soft dihedrals in an iteration way (consistent with charmm36 and CGenFF philosophy). The output files also include modified angle,

[gmx-users] Lattice distance for HII phase

Dear Gromacs users, I have a HII phase made of molecules. HII phase is formed of many cylinders parallel to z axis (in my case) in a hexagonal geometry. I am interested in calculating the distance between these cylinders. I want to have a more accurate statistical way to measure it. So, I think

[gmx-users] Fwd: self-assembly and box size

Dear Gromacs users, I have made an initial system with a number of molecules in a "large" box. Large means a box of size 50 50 50 nm? I am interested in the self-assembly process of molecules (parametrized in charmm36 ff) in the box. I expected pressure coupling to shrink the box quickly,

[gmx-users] using implicit water for atomistic simulation of lipid bilayer

Dear Gromacs Users, I was wondering if there is any example of using Implicit water model for lipid bilayers in Gromacs? I have read on using implicit solvents in Gromacs and found interesting discussions: https://groups.google.com/forum/#!topic/archive-gmx-users/0HIFVop390I

Re: [gmx-users] using implicit water for atomistic simulation of lipid bilayer

Thanks Justin. Agreed. I wanted to make sure about that. Cheers On Sat, Dec 10, 2016 at 12:48 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/9/16 5:58 PM, Mohsen Ramezanpour wrote: > >> Dear Gromacs Users, >> >> I was wondering if there is any e

Re: [gmx-users] Lattice distance for HII phase

For whom this might have been a question: Given a HII phase with cylinders parallel to z direction, simulation box size in x and y-direction will give the cell size the lattice distance (d_hex), respectively. Cheers Mohsen On Thu, Dec 1, 2016 at 11:20 AM, Mohsen Ramezanpour < ramezanpour.

Re: [gmx-users] MM dihedral scanning

1:20 PM, Mohsen Ramezanpour wrote: > >> On Thu, Jan 12, 2017 at 8:36 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 1/12/17 10:21 PM, Mohsen Ramezanpour wrote: >>> >>> On Thu, Jan 12, 2017 at 6:31 PM, Justin Lemkul <jalem...

Re: [gmx-users] Fwd: LJ cut-offs

There is a great discussion which is relevant and better to read. https://github.com/NMRLipids/NmrLipidsCholXray/issues/4 Cheers Mohsen On Wed, Jan 11, 2017 at 10:46 AM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Guys, > > Thanks for your comments. My question w

Re: [gmx-users] Fwd: LJ cut-offs

; On 1/11/17 12:46 PM, Mohsen Ramezanpour wrote: > >> Hi Guys, >> >> Thanks for your comments. My question was exactly what Dawid clarified. >> Sure, I will read those as you suggested. >> >> Dawid, regarding this: >> "You need to keep in mind however

Re: [gmx-users] rlist, rcolumb, and rvdw

forcefield and should not be varied without extensive testing. See >>>> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM >>>> >>>> >>> To emphasize, this is especially true for CHARMM lipid parameters, as is >>> the >>> case h

Re: [gmx-users] Fwd: LJ cut-offs

his is why. Cheers Mohsen On Wed, Jan 11, 2017 at 5:54 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/10/17 10:40 PM, Mohsen Ramezanpour wrote: > >> Dear gromacs users, >> >> Please let me know your opinion on the following question: >> Thanks in

[gmx-users] rlist, rcolumb, and rvdw

Dear gromacs users, Reading through mailing list I found a nice discussion on the relation between rlist, rcolumb, and rvdw: https://www.mail-archive.com/gmx-users@gromacs.org/msg08387.html https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-February/058507.html If I understood

Re: [gmx-users] MM dihedral scanning

(as it is the case for charmm36 ff). Please let me know your opinion. Cheers Mohsen On Thu, Jan 12, 2017 at 8:21 PM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > On Thu, Jan 12, 2017 at 6:31 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 1/12/

Re: [gmx-users] MM dihedral scanning

On Thu, Jan 12, 2017 at 4:24 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/12/17 3:18 PM, Mohsen Ramezanpour wrote: > >> Dear Gromacs users, >> >> For parameterization of a molecule in Charmm36, I have got the QM scanning >> and partial char

Re: [gmx-users] MM dihedral scanning

On Thu, Jan 12, 2017 at 6:31 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/12/17 7:47 PM, Mohsen Ramezanpour wrote: > >> On Thu, Jan 12, 2017 at 4:24 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 1/12/17 3

Re: [gmx-users] MM dihedral scanning

On Thu, Jan 12, 2017 at 8:36 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/12/17 10:21 PM, Mohsen Ramezanpour wrote: > >> On Thu, Jan 12, 2017 at 6:31 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 1/12/17 7:47 PM,

[gmx-users] MM dihedral scanning

Dear Gromacs users, For parameterization of a molecule in Charmm36, I have got the QM scanning and partial charges from GAMMP server. However, the fitted parameters are not good enough. I decided to do the MM scanning and try to get better parameters for the dihedral. Unfortunately, I do not

[gmx-users] Fwd: LJ cut-offs

Dear gromacs users, Please let me know your opinion on the following question: Thanks in advance for your comments -- Forwarded message -- From: Mohsen Ramezanpour <ramezanpour.moh...@gmail.com> Date: Thu, Jan 5, 2017 at 5:20 PM Subject: LJ cut-offs To: Discussio

Re: [gmx-users] Lattice distance for HII phase

Dear gromacs users, I appreciate your opinion on this email in advance. Cheers Mohsen On Thu, Nov 17, 2016 at 11:07 AM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Dear Gromacs users, > > I have a HII phase made of molecules. HII phase is formed of many >

[gmx-users] order parameters for Inverted hexagonal phase

Dear Gromacs Users, I have a question on how to use g_order to get the order parameters correctly for an inverted hexagonal (HII) phase and compare it with experimental values from NMR. I read some articles, including following one: Vermeer, Louic S., et al. "Acyl chain order parameter profiles

[gmx-users] Order Parameter with an all-atom force field

Dear Gromacs users, I have a question on S_cd order parameters: Using g_order for a lipid like DSPC, I can get the values for C2 to C17, although DS tail has 18 carbons. I know the reason when I use a united atom force field like Gromos54A7. This is mainly based on the algorithm which it works

[gmx-users] adding new parameters to force field

Dear Gromacs users, I have a new file with both bonded and nonbonded parameters for some atom types in it. I want to use these new parameters for simulation and ignore the parameters in force field ( if there is any parameter already exist). 1) If I add the lines from each section of new file at

Re: [gmx-users] adding new parameters to force field

> Sometimes. It depends exactly which functions and function types, and > whether it's part of a moleculetype. If you don't want something, don't > include it :-) > > Mark > > On Thu, 22 Dec 2016 10:07 Mohsen Ramezanpour <ramezanpour.moh...@gmail.com > > > wrote: &

Re: [gmx-users] Problem with combining the .edr files

edr is > actually smart enough to perhaps stop you doing something that isn't > useful. > > Mark > > On Wed, Mar 15, 2017 at 7:26 PM Mohsen Ramezanpour < > ramezanpour.moh...@gmail.com> wrote: > > > Dear Gromacs users, > > > > I did a simulation in

[gmx-users] Problem with combining the .edr files

Dear Gromacs users, I did a simulation in parts using -noappend command, so I have a few .trr and .edr files which I wish to merge. I have difficulty with that and I could not find any related post on that except this one: http://comments.gmane.org/gmane.science.biology.gromacs.user/68806 Using

Re: [gmx-users] gmx hbond

kl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> > > On 14 Apr 2017, at 03:20, Mohsen Ramezanpour <ramezanpour.moh...@gmail.com > <mailto:ramezanpour.moh...@gmail.com>> wrote: > > Hi Gromacs users, > > I have a question regarding the output file from

[gmx-users] gmx hbond

Hi Gromacs users, I have a question regarding the output file from g_hbond: First:I have done my simulations with version 4.6.7 and doing the analysis with version 2016.2 Will this cause any hidden problem in analysis? the analysis is working fine but I am asking about the correctness of results

Re: [gmx-users] Gromac4.6.7 installation problem

arallel make obscures problems when they exist, so run again with > simple make. Probably cuda does not support your compiler, so you will run > into problems later. I suggest gcc 4.9 > > Mark > > On Thu, 2 Mar 2017 06:58 Mohsen Ramezanpour <ramezanpour.moh...@gmail.com

[gmx-users] reading topology by Gromacs

Dear Gromacs users, I want to add the modified parameters for several proper dihedrals. So, I want to add them to the section [ dihedraltypes ] in ffbonded.itp. There are two dihedrals already for the combination I want: C HC HC NC2 2 0.00 0.00 . . . NC2

Re: [gmx-users] Atom types comparison between CGenFF and Charm36FF

wrote: > > > On 6/27/17 3:27 PM, Mohsen Ramezanpour wrote: > >> Dear Gromacs Users, >> >> I am trying to parameterize a molecule in Charmm36FF. >> >> As part of this molecule, there is a "neutral trimethylamine nitrogen" and >> its protonated case.

[gmx-users] Atom types comparison between CGenFF and Charm36FF

Dear Gromacs Users, I am trying to parameterize a molecule in Charmm36FF. As part of this molecule, there is a "neutral trimethylamine nitrogen" and its protonated case. i.e. C-N-C(2) and C-N(H)-C(2), respectively. To have some idea about the appropriate atom types, I first used the GAAMP

Re: [gmx-users] Atom types comparison between CGenFF and Charm36FF

Thanks, Justin. Sure. On Wed, Jun 28, 2017 at 10:21 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/28/17 9:10 AM, Mohsen Ramezanpour wrote: > >> Thanks Justin for your comment. >> >> I have a bit of difficulty for the finding the analog parts to th

[gmx-users] GAAMP parameterization

Dear Gromacs users, Using GAAMP server for parameterization, if the GAFF for "initial parameters" is used instead of "CGenFF": 1) Can the results still be used for using simulation in "Charmm36" force field? Assuming that all the other values are chosen as default ones in the GAAMP webpage. 2)

[gmx-users] PBC fix for visualization

Dear Gromacs users, I have an HII phase made of one inverted cylinder (and waters inside) in a triclinic box with 90, 90, 60 angles. After running the simulation, this cylinder become bent like a curve. I.e. is not a perfect cylinder anymore. As a result, some water molecules and lipids pass the

Re: [gmx-users] PBC fix for visualization

> When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On 16 May 2017 at 07:50, Mohsen Ramezanpour > <ramezanpour.moh...@gmail.com> wrote: > > Dear Gromacs users, > > > > I have an HII phase made of one inverted cyli

Re: [gmx-users] RMSF per residue

otal number of atoms in this selection. Thanks Mohsen On Thu, May 25, 2017 at 12:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/24/17 4:12 PM, Mohsen Ramezanpour wrote: > >> Dear Gromacs users, >> >> I have a question on RMSF calculation: >> >>

Re: [gmx-users] RMSF per residue

, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Thanks Justin! > > On Thu, May 25, 2017 at 12:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 5/24/17 4:12 PM, Mohsen Ramezanpour wrote: >> >>> Dear Gromacs users, &g

[gmx-users] auto correlation function and time

Hi guys, I have a quick question on calculating the autocorrelation time: I have the file for a dihedral angle vs time (named angle.xvg). Now, I need to calculate the autocorrelation time for this angle. There are two problems, though: 1) If I use the angle.xvg with g_angle itself (i.e. using

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