[gmx-users] WARNING: Listed nonbonded interaction between particles X and Y at distance

Dear all, I am trying to perform free energy calculations of a small drug in octanol using the GROMACS 5.1.3 software. I built a box of octanol using the following command gmx insert-molecules -ci oct.gro -nmol 125 -box 4 4 4 -o oct_box.gro Followed by steepest descent minimization, 100 ps each

[gmx-users] How to find the loading capacity of a nanostructure?

Dear all, I have performed 50 ns of production MD simulation on a polymer that contains several drug molecules. Now I need to find how many drugs (and which ones) remain encapsulated into the polymer. I measured the COM separation distance between polymer and each drug. However, the problem is

[gmx-users] How to find the loading capacity of a nanostructure?

Dear all, I have performed 50 ns of production MD simulation on a polymer that contains several drug molecules. Now I need to find how many drugs (and which ones) remain encapsulated into the polymer. I measured the COM separation distance between polymer and each drug. However, the problem is

[gmx-users] Drug moves out of the nanocarrier

Dear Gromacs users, I am trying to perform PMF calculations on a nanocarrier-drug system. The procedure I have performed is as follows: 1) running MD simulation on the unloaded nanocarriers for 30 ns 2) insertion of drug into nanostructure using AutoDock 3) running production MD simulation on the

[gmx-users] Drug moves out of the nanocarrier

Dear Gromacs users, I am trying to perform PMF calculations on a nanocarrier-drug system. The procedure I have performed is as follows: 1) running MD simulation on the unloaded nanocarriers for 30 ns 2) insertion of drug into nanostructure using AutoDock 3) running production MD simulation on the

[gmx-users] Adding a number of drugs around a polymer

Dear GROMACS users, I need to locate a number of drug molecules around one equilibrated polymer molecule and drugs should be randomly located within a spherical shell from the polymer surface. Will be greatly appreciated if help me on that. Regards, Farideh -- Gromacs Users mailing list *

[gmx-users] Pulling occurs in the smaller side of reaction coordinate

Dear Gromacs users, I have a question regarding generating configurations in US simulations. I have generate 500 frames in the z-direction. However, pulling does not occur in the larger side of the box. The ligand leaves the box from the smaller side and then enters from the other side. Does it

Re: [gmx-users] Farideh Khamseh shared "profileNH2.xlsx" with you

Dear Erik, The file I shared is PMF profile that I have obtained performing US simulations and I do not know why it goes down after 2 nm separation distance between polymer and ligand. Regards, Farideh On Thu, Jan 26, 2017 at 12:05 PM, faride badalkhani < farideh.kham...@gmail.com> wrote:

Re: [gmx-users] Problem with the autocorrelation of Rg

help me on this issue? You can find the profile in the following link: https://www.dropbox.com/s/8k1e0eqm80osg7j/profileNH2.xlsx?dl=0 Regards, Farideh On Mon, Jan 23, 2017 at 11:47 PM, faride badalkhani < farideh.kham...@gmail.com> wrote: > Dear Erik, > > Thank you so mu

Re: [gmx-users] Problem with the autocorrelation of Rg

led to contain any trace of “memory” in the > system. Have you tried calculating the act by other means, xmgrace for > instance? Does that yield a similar result? > > Kind regards, > Erik > > > On 23 Jan 2017, at 12:08, faride badalkhani <farideh.kham...@gmail.

Re: [gmx-users] Problem with the autocorrelation of Rg

gt; > Thanks. And the file Rg.xvg looks sound? > > Kind regards, > Erik > > > On 23 Jan 2017, at 11:33, faride badalkhani <farideh.kham...@gmail.com> > wrote: > > > > Hi, > > > > Thanks for the answer. I used the autocorrelation function of the squ

Re: [gmx-users] Problem with the autocorrelation of Rg

, 2017 at 1:42 PM, Erik Marklund <erik.markl...@kemi.uu.se> wrote: > Dear Farideh, > > Can you please inform us about how you calculated the ac? Hard to help > otherwise. Also, is it exactly zero or just very small numbers? > > Kind regards, > Erik > > > On 23 J

[gmx-users] Problem with the autocorrelation of Rg

Dear GROMACS users, I am performing umbrella sampling on a polymer-ligand system and I generate configurations successfully but the problem is that when I plot the autocorrelation function of Rg for each window it is zero for the whole time of simulation. I changed the run time for each window

[gmx-users] Problem with the autocorrelation of Rg

Dear GROMACS users, I am performing umbrella sampling on a polymer-ligand system and I generate configurations successfully but the problem is that when I plot the autocorrelation function of Rg for each window it is zero for the whole time of simulation. I changed the run time for each window

[gmx-users] window spacing in umbrella sampling

Dear GROMACS users, I have performed pulling simulations on polymer-drug complex an each window was obtained by an increment of 1 Å from the previous window, and for each window, 5 ns MD simulation was performed. But the histogram for the first 6 windows is as follows:

[gmx-users] The Rg does not change during the umbrella sampling

Dear all, I want to perform pulling simulations on a polymer-drug system. I have performed simulations on polymer and polymer+drug for 30 ns and then set up system for pulling. After generating configurations I chose some of them and performed a 10 ns of MD for each window. However, when I plot

[gmx-users] The Rg does not change at all during the umbrella sampling

Dear all, I want to perform pulling simulations on a polymer-drug system. I have performed simulations on polymer and polymer+drug for 30 ns and then set up system for pulling. After generating configurations I chose some of them and performed a 10 ns of MD for each window. However, when I plot

[gmx-users] autocorrelation function

Dear Gromacs users, I calculate autocorrelation function of Rg using the following command: gmx analyze -f gyrate.xvg -o ac now I have two questions: 1) when I obtain Rg there are 3 columns in the file including Rg, Rg x, Rg y, and Rg z, respectively. Is this trend correct for the acf file,

[gmx-users] Desired spacing in umbrella sampling

Dear Gromacs users, Is it reasonable to choose asymmetric windows in umbrella sampling? I want to use 0.1 nm spacing for 0.6-2.6 COM distance and then 0.2 nm for 2.6-5.3. Regards, Farideh -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Production run before starting Pulling

Dear Gromacs users, I want to perform center of mass pulling simulations on a nanostructure-drug structure. I performed MD simulations on the nanostructure for 30 ns and it equilibrated well. then I docked the drun into the nanostructure using Auto Dock Vina software. Now I want to know if I

Re: [gmx-users] The time need for each window in umbrella sampling

hough the later will probably be a pain with PMFs). > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of faride > badalkhani <farideh.kham...@gmail.com> > Se

[gmx-users] The time need for each window in umbrella sampling

Dear Gromacs users, Is there any criteria tk determine tge optimum run time for each window in umbrella sampling? My receptor has equilibrated after 30 ns of MD. Should I consider the same run time for each window? Regards, Farideh -- Gromacs Users mailing list * Please search the archive at

[gmx-users] The time need fir each window in umbrella sampling

Dear Gromacs users, Is there any criteria tk determine tge optimum run time for each window in umbrella sampling? My receptor has equilibrated after 30 ns of MD. Should I consider the same run time for each window? Regards, Farideh -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Orienting molecule in a correct direction

box dimensions or just z dimension? Regards, Farideh On Sun, Oct 30, 2016 at 7:50 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/30/16 12:03 AM, faride badalkhani wrote: > >> Dear all, >> >> I want to define z axis as the reaction coordinate in a ser

[gmx-users] Orienting molecule in a correct direction

Dear all, I want to define z axis as the reaction coordinate in a series of umbrella sampling simulations. As a first step, I use the editconf -prince to orient the ligand along the x axis and then I change the x and z columns in an editor. But, every time I get error at pulling step. Could you

[gmx-users] Pulling error

Dear all, I am very beginner in PMF calculations and I want to set up a nanostructure-drug system for umbrella sampling. To define the unit cell I used the -princ option in editconf command line,and then I changed the y and z columns in an editor to fix the reaction coordinate in z direction.

[gmx-users] Problem with Charges

Dear all, I have parameterized a relatively large molecule (136 atom) with PRODRG server, and then I assigned charges and charge groups in a building bock style manner. I know that my system include a total +8 charge, but when I execute genbox command i receive the following note: System total

Re: [gmx-users] energy minimization error

that there > are bonds exactly where you intend them, before doing any calculations with > them. > > Mark > > On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani < > farideh.kham...@gmail.com> > wrote: > > > Hi, > > > > I am trying to simulate a hype

[gmx-users] energy minimization error

Hi, I am trying to simulate a hyper-branched polymer (a dendrimer) in water. But, every time the system blows up at energy minimization step. Therefore, according to what Mark had recommended I decided to start with a much smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had

Re: [gmx-users] Energy minimization error

simpler than a multiply branched > dendrimer. Join two units with a specbond, inspect the .top so that you > know it has what you think it has, and get that to EM and simulation > stably. Then you can get more complex. > > Mark > > On Sat, Oct 17, 2015 at 3:58 PM faride bada

Re: [gmx-users] Energy minimization error

elp is appreciated. On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Look at atom 380 and see why the forces might be high. > > Mark > > On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani < > farideh.kham...@gmail.com> >

[gmx-users] Energy minimization error

Thank you for your great help on specbond.dat file. I defined it and I could go ahead until Energy minimization step. I have used this minim.mdp file ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep

Re: [gmx-users] bond, angles and dihedrals in the topology file

eps for a few times. However, I couldn't resolve this problem. Could you tell me if there is something wrong with the minim.mdp file? You can see all the files via: https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0 Truly yours, Farideh On Wed, Sep 30, 2015 at 9:13 PM, faride badalk

[gmx-users] bond, angles and dihedrals in the topology file

Dear all, Could you tell me what is wrong when there are some strange bond, angles and dihedrals in the topology file after executing pdb2gmx command? for example atoms 1 and 27 do not have any connectivity, but pdb2gmx generate them as [bonds]. A similar problem occurs in case of angles and

Re: [gmx-users] bond, angles and dihedrals in the topology file

. you can see all the files via https://www.dropbox.com/s/c8csnchfdahe016/4MEHR.zip?dl=0 Excuse me for my poor English, Truly yours, Farideh On Wed, Sep 30, 2015 at 3:03 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/30/15 7:21 AM, faride badalkhani wrote: > >> D

Re: [gmx-users] bond, angles and dihedrals in the topology file

for one such example. > > Chandan > > On Wed, Sep 30, 2015 at 8:29 PM, faride badalkhani < > farideh.kham...@gmail.com> wrote: > >> Thank you for your time and answer. You are right, Dendrimers are composed >> of three main architectural components, a central core fr

Re: [gmx-users] bond, angles and dihedrals in the topology file

specbond file for hyperbranched polymers? Regards, Farideh On Wed, Sep 30, 2015 at 6:07 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/30/15 8:24 AM, faride badalkhani wrote: > >> I want to simulate a dendrimer (a hyperbranched polymer) in water. I have >> us

[gmx-users] grompp error

Dear GROMACS users, I need to simulate a hyper branched polymer (a polyamidoamine dendrimer). I used the GROMOS53A6 to perform the simulation. But, I have a problem with defining the angles and dihedrals that are between two residues (because of dendrimers hyper branched structure). I can perform

[gmx-users] bonds, angles, and dihedrals in .rtp file format

Dear Gromacs users, I want to know if it is mandatory to add bonds, angles, and dihedrals in the .rtp file for a novel residue? According to Gromacs manual you need to add atoms and charges, only. Truly yours, Farideh -- Gromacs Users mailing list * Please search the archive at

[gmx-users] em.gro file doesnt show a reasonable structure in VMD

Dear gmx users, I have perform an energy minimization on my system and the potential per step plot has a normal appearance, but the em.gro file doesn't show a reasonable structure in VMD. Could you tell me why this happened? Regards, Farideh -- Gromacs Users mailing list * Please search the

Re: [gmx-users] em.gro file doesnt show a reasonable structure in VMD

structure reasonable? Upload a screenshot to a file sharing service and show us what you think is unreasonable :-) Mark On Tue, Aug 25, 2015 at 12:16 PM faride badalkhani farideh.kham...@gmail.com wrote: Dear gmx users, I have perform an energy minimization on my system

[gmx-users] GROMOS atp file

Dear all, I am having a question about Hydrogens in GROMOS FF. There are two Hysrogens in .atp file of GROMOS FF as follows: HC 1.00800 ; hydrogen bound to carbon H 1.00800 ; hydrogen not bound to carbon and all the nonbonded parameters for H are considered zero, but what

Re: [gmx-users] GROMOS atp file

But all the nonbonded parameters for these Hydrogens are zero while they are polar and they should be considered On Sat, Aug 15, 2015 at 4:17 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/15/15 4:42 AM, faride badalkhani wrote: Dear all, I am having a question about Hydrogens in GROMOS FF

Re: [gmx-users] GROMOS atp file

Thanks a lot for your time and patience. Truly yours, Farideh On Sat, Aug 15, 2015 at 6:24 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/15/15 9:51 AM, faride badalkhani wrote: But all the nonbonded parameters for these Hydrogens are zero while they are polar and they should

[gmx-users] pdb file for united atom force fields

Dear Gromacs users, I need to work with a united atom FF, but I have defined all the Hydrogens in my pdb file. Does it cause any problem in MD procedure? Truly yours, Farideh -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Blowing up

groups and run the dynamics again. Hope this helps Victor 2015-08-09 2:16 GMT-05:00 faride badalkhani farideh.kham...@gmail.com: Dear all, I am truing to do an MD simulation on dendrimeric structures. I can perform all steps successfully, but I get a NOTE in all steps after Adding

[gmx-users] Blowing up

Dear all, I am truing to do an MD simulation on dendrimeric structures. I can perform all steps successfully, but I get a NOTE in all steps after Adding Ions as follows: NOTE 2 [file topol.top]: The largest charge group contains 20 atoms. Since atoms only see each other when the centers of

[gmx-users] pdb2gmx error

Dear all, could anybody help me at this error? Fatal error: atom N not found in buiding block 1AMC while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Kind regards, Farideh -- Gromacs

[gmx-users] pdb2gmx warning

Dear all, I am performing a simulation on a plymeric structure, and I can exwcute pdb2gmx command successfully but there are some warnings as follows: Warning: Starting residue AMC1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue AMI2 in chain not identified as

[gmx-users] adding a new residue to residuetypes.dat

Dear all, According to GROMACS Manual, we should add the residue name to the residuetypes.dat file when we are adding a new residue to the database. But. I am having a question in this regard. I need to add some residues pertaining to a polymer. Should I consider these residues as protein

Re: [gmx-users] Problem in .gro file

Hi, I have shared the files via Dropbox https://www.dropbox.com/sh/bp3d1ugn233domy/AACSSs8fFCmXn_MBRjZBheoda?dl=0 On Wed, Jul 8, 2015 at 4:54 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/7/15 9:13 AM, faride badalkhani wrote: Dear Justin, This is the link you can find the prepared

Re: [gmx-users] Problem in .gro file

Dear Justin, This is the link you can find the prepared files: http://www.4shared.com/zip/HpM1O820ce/FF_online.html Truly yours, Farideh On Wed, Jul 1, 2015 at 2:57 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/30/15 6:12 PM, faride badalkhani wrote: I cannot understand what do you mean

[gmx-users] Problem in .gro file

Dear all, I am trying to simulate a hyperbranced polymer (a dendrimer) with gromacs. Therefore, I have parametrized the GROMOS 53A6 FF, and executed pdb2gmx, and got a command as follows: You have successfully generated a topology from : G3-Neutral.pdb The Pamam force field and the spce water

Re: [gmx-users] Problem in .gro file

, faride badalkhani wrote: Dear all, I am trying to simulate a hyperbranced polymer (a dendrimer) with gromacs. Therefore, I have parametrized the GROMOS 53A6 FF, and executed pdb2gmx, and got a command as follows: You have successfully generated a topology from : G3-Neutral.pdb The Pamam force

[gmx-users] Saving Changes in FF files

Dear gmx-users, I am having a question about saving changes in .atp, .itp, and .rtp files in GROMOS53A6 force field. I know it may be a strange question for you, but I am a beginner at FF parametrization, and I cannot save the changes that I need in mentioned files. Truly yours, Farideh --

[gmx-users] specbond files

Dear all, I need to use specbond.dat file for a branched polymer, but I do not know what is the meaning of: the new name for residue A and the new name for residue B! Could you help me with this? Truly yours, Farideh -- Gromacs Users mailing list * Please search the archive at

[gmx-users] How to connect different parts of a polymer?

Dear GMX users I am trying to parametrize GROMOS FF for PAMAM dendrimers. I have paramerized core of the dendrimer, its repeat units, and terminal groups separately. but I dont know how to connect them to build a complete dendrimer so that GROMACS can recognize dendrimer structure exactly. Could

[gmx-users] Force field parameterization for PAMAM dendrimers

Dear all, I want to perform MD simuations on PAMAM dendrimers, but unfortunately this molecule has not been defined in any of the GROMACS force fields. Therefore, I should parameterize the force field for my purpose. How should I do this procedure? (It is mentionable that I read the

[gmx-users] Appropriate Force Field for Dendrimer-Drug Systems

So, is it possible for me to use GROMACS package for my project? -- 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] Appropriate Force Field for Dendrimer-Drug Systems

Dear all, I am going to investigate the interaction between poly(amidoamine) dendrimers with different generations, cores, and surface groups (NH2, COOH, OH, etc) and some low soluble drugs such as curcumines and chalcones. So, I should perform a productive MD run on the dendrimer nanostructures