Re: [gmx-users] Aggregation or phase separation

tion and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On 10 O

[gmx-users] Aggregation or phase separation

I am using Gromacs to study the cis-pinonic acid aggregation in water. In order to use the Gibbs-duhem relation, I would like to know if these aggregates form inside the water are pseudo-phase or separate phase? Do you have any hint how to define the phase of aggregates in water by using Gromacs

[gmx-users] Differentiate of aggregation of precipitation in MD simulation

Dear all, I am simulation the aggregation of HULIS like molecule. However I would like know if there is way in Gromacs to analyse if these bunch of molecules gather together because of aggregation or precipitation? Bests -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Display error bars for traj

Dear all, I use g_traj command to extract the z-coordinate of the molecules from .xtc files. I wonder is there a way to display also the error bars for these coordinates? Bests -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] units of gmx wham output

Capital {S-1} is to make it ^{-1}. It is for superscript. And the \N returns the text to the default state. So it is basically the y-axis name for xmgrace tool. If you plot your .xvg file by using xmgrace you will see kj/mol on your Y-axis title. Overall your energy unit is kj/mol which is

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

clearly suggests putting it in the ffnonbonded.itp file, which is where you > expected to find it at the start of this thread, right? :-) > > Mark > > On Thu, Jun 22, 2017 at 3:47 PM gozde ergin <gozdeeer...@gmail.com > <mailto:gozdeeer...@gmail.com>> wrote: > >> Hey Ju

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

topol.top, line 42 Last line read: '[ nonbond_params ]' Invalid order for directive nonbond_params Any suggestion would be appreciated. > On 21 Jun 2017, at 16:46, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 6/21/17 10:39 AM, gozde ergin wrote: >> Hi MArk, &

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

; > > On 6/21/17 10:39 AM, gozde ergin wrote: >> Hi MArk, >> Thanks for the respond. I understood that point however I still do not get >> which sigma to change. >> I the paper JCTC 2017, Miller et. al. they have mentioned that they increase >> the for

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

d > differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma > is a property of the atomtype > > Mark > > On Wed, Jun 21, 2017 at 4:16 PM gozde ergin <gozdeeer...@gmail.com> wrote: > >> Dear users, >> >> I am trying to change th

[gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

Dear users, I am trying to change the sigma value of amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS. However I have difficulties to understand which parameter i should change in ffnonbonded.itp file? I am looking something like [ nonbond_params ] section however it is not

Re: [gmx-users] extract the coordinate by using traj command for sphere system

Thanks Justin ! > On 12 Jun 2017, at 14:01, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 6/12/17 7:59 AM, gozde ergin wrote: >> But I need to understand if atoms go beyond the wall (flat-bottom restraint). >> In order to understant that I need to k

Re: [gmx-users] extract the coordinate by using traj command for sphere system

;jalem...@vt.edu> wrote: > > > > On 6/12/17 4:36 AM, gozde ergin wrote: >> Dear all, >> In order to calculate the osmotic pressure I would like to extract the >> coordinate of my atoms by using g_traj command. >> Before my box was cubic and by using >>

[gmx-users] extract the coordinate by using traj command for sphere system

Dear all, In order to calculate the osmotic pressure I would like to extract the coordinate of my atoms by using g_traj command. Before my box was cubic and by using gmx_mpi traj -f nvt.trr -s nvt.tpr -n index.ndx -ox coord-atoms.xvg -nox -noy I was getting coordinate of all of my atoms in

Re: [gmx-users] powercut command

Lincs warning usually occurs for the system that not minimized. You can try to minimize your system before running the real simulation. Other option would be use -maxwarn flag but please use it only if you know that these warnings are not important. > On 13 Apr 2017, at 11:10, Anshul Lahariya

Re: [gmx-users] Replica Exchange for surface tension

optimization however they used amine groups and betaine has tetramethylamine group. Thanks in advance. > > > > On 3/28/17 2:59 PM, gozde ergin wrote: >> I use Charmm36 force field. Do you mean the force field parameter between >> cocobetaine and SDS? Because for pure surfacta

Re: [gmx-users] Replica Exchange for surface tension

) and under NVT ensemble? > On 29 Mar 2017, at 15:21, gozde ergin <gozdeeer...@gmail.com> wrote: > > Exactly SDS is CHARMM36 but cocobetaine not. > >> On 29 Mar 2017, at 15:18, Justin Lemkul <jalem...@vt.edu >> <mailto:jalem...@vt.edu>> wrote: >>

Re: [gmx-users] Replica Exchange for surface tension

Exactly SDS is CHARMM36 but cocobetaine not. > On 29 Mar 2017, at 15:18, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 3/29/17 9:16 AM, gozde ergin wrote: >> Are you sure it is not CHARMM36 because it is written: >> >> ;; >> ;; Generated b

Re: [gmx-users] Replica Exchange for surface tension

:06, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 3/29/17 4:15 AM, gozde ergin wrote: >> I used CHARMM GUI Input Generator tool both for SDS and cocobetaine. > > For the sake of clarity, you should understand that you are *not* then using > CHARMM36.

Re: [gmx-users] Replica Exchange for surface tension

kul <jalem...@vt.edu> wrote: > > > > On 3/28/17 2:59 PM, gozde ergin wrote: >> I use Charmm36 force field. Do you mean the force field parameter between >> cocobetaine and SDS? Because for pure surfactant I am able to estimate the >> correct surface tension. W

Re: [gmx-users] Replica Exchange for surface tension

017, at 7:21 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > >> On 3/28/17 12:43 PM, gozde ergin wrote: >> I have a mixed system of SDS and cocobetaine on water surface. >> I estimated the surface tension of SDS on water surface and cocabetaine on >> surface t

[gmx-users] Replica Exchange for surface tension

I have a mixed system of SDS and cocobetaine on water surface. I estimated the surface tension of SDS on water surface and cocabetaine on surface tension separately and correctly (comparing with experimental results). However I could not estimate the correct surface tension for SDS-cocobetaine

[gmx-users] mindist in gromacs

Dear all, I am trying to calculate the minimum distance between head groups on the water surface. I used the gmx mindist tool in Gromacs however I am not sure what is the meaning of this distance? Is it the distance according to x or y or z axis? Or is there a way to estimate the minimum

Re: [gmx-users] Potential energy in Zwanzig relationship

; On Fri, Feb 10, 2017 at 5:26 AM, gozde ergin <gozdeeer...@gmail.com> wrote: > >> Dear all, >> >> I run thermodynamic integration simulation with gromacs and got the free >> energy by g_bar command. >> I also would like to estimate this free energy by using

[gmx-users] Potential energy in Zwanzig relationship

Dear all, I run thermodynamic integration simulation with gromacs and got the free energy by g_bar command. I also would like to estimate this free energy by using Zwanzig relationship of \DeltaG = -RT ln (_i Here U is the potential energy, right? However the results

Re: [gmx-users] g_wham PMF Profiles

Hi Zeynep, As you exclude the window, you lost the local information. But even excluded PMF profile does not seem that ’smooth’. What is your simulation time? And maybe you may think of pulling slower like 0.01 nm spacing. bests (iyi calismalar) > On 10 Feb 2017, at 08:57, ZEYNEP ABALI

Re: [gmx-users] Segmentation fault in MDRUN

You may try with dt = 0.001. Also maybe you can increase the equilibration time. On 25 Jan 2017, at 09:30, Matteo Busato wrote: > > dt = 0.002 -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] G_ENERGY COMMAND

gmx energy should be the correct command. > On 13 Jan 2017, at 10:53, Subashini .K wrote: > > > Hi gromacs users, > > > I am using gromacs in windows 7, 64 bit. > > > When the following command was given, > > > gmx g_energy -f ener.part0001.edr -o vol.xvg > > >

Re: [gmx-users] Questions about free energy calculation tutorial

-0.8 in vow-lambda values). Do you have any idea why I could not see any minima or should I see a minima? Thanks in advance. > On 13 Nov 2016, at 13:19, gozde ergin <gozdeeer...@gmail.com> wrote: > > Hi all, > > I tried to estimate the free energy of betaine on betain

Re: [gmx-users] Questions about free energy calculation tutorial

strange that I have very big numbers on x axis (like e+33). Please see the plots link below. https://imgur.com/a/fqgmi Any help would be appreciated. Thanks. > On 06 Nov 2016, at 14:33, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 11/6/16 8:27 AM, gozde ergin w

Re: [gmx-users] Umbrella Sampling

Hey, Did you change the number inside the distances.pl script? If you have 1000 files, you need to change the number of 500 on line 6, 13 , and 36 (lines start with for loop) make them 1000. > On 13 Nov 2016, at 11:10, Mouri Ahmed wrote: > > Hi everyone, > > I have

[gmx-users] MBAR issue

Dear all, I follow James Barnett tutorial of “Methane Free Energy of Solvation” however I use betaine molecule other than methane. In order to analyse the data I use alchemical_analysis.py code however I get an error : pymbar.utils.ParameterError: Warning: Should have \sum_k N_k W_nk = 1.

Re: [gmx-users] Questions about free energy calculation tutorial

Thanks a lot Justin, Everything is more clear right now. Bests > On 06 Nov 2016, at 17:30, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 11/6/16 10:44 AM, gozde ergin wrote: >> >>> This may be unstable, and is generally not done. Turn off ch

Re: [gmx-users] Questions about free energy calculation tutorial

> This may be unstable, and is generally not done. Turn off charges linearly, > then turn off LJ with a soft-core potential (or vice versa). The point is > you should never have charges on atoms with no (or drastically reduced) LJ > terms. This can be easily specified in an appropriate

Re: [gmx-users] Questions about free energy calculation tutorial

> If it's the salt, then take the known Na+ value for the force field and add > it to the SDS value you obtain at infinite dilution. Straightforward. Ok either I can take hydration free energy of Na from the literature or I can run 2 thermodynamic integration with dodecyl sulfate and Na

Re: [gmx-users] Questions about free energy calculation tutorial

> If you need the total free energy of hydration for NaSDS, you can just > decouple SDS in water with no Na+ and sum the two contributions (SDS and Na+ > separately). If you just want the SDS hydration free energy, decouple it in > a box of pure water Thanks Justin, I have difficulty to

Re: [gmx-users] Questions about free energy calculation tutorial

Thank Justin, ok I understand now. Then I need to run the simulation with +1 charge, since I made 0 of all the charges in SDS, Na+ charge will stay there. Do you think it is ok run with +1 charge? > On 04 Nov 2016, at 13:36, Justin Lemkul wrote: > > No, you should not. The

Re: [gmx-users] Questions about free energy calculation tutorial

if I only write SDS to couple-moltype in .mdp file, it will decouple C12H25SO4- but not Na+. Should I put Na+ atom inside the SDS.itp? > On 04 Nov 2016, at 12:51, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 11/3/16 10:56 AM, gozde ergin wrote: >>> You can decou

Re: [gmx-users] Questions about free energy calculation tutorial

ecoupling, is it wrong? > On 02 Nov 2016, at 12:42, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 11/1/16 9:02 AM, gozde ergin wrote: >>>> This is a generic simulation failure message, indicating that your system >>>> is blowing up. This could b

Re: [gmx-users] Questions about free energy calculation tutorial

. > On 01 Nov 2016, at 13:21, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 11/1/16 7:31 AM, gozde ergin wrote: >> Hi Justin, >> >> I would like to ask one question related to this tutorial. I do the same >> thing with using SDS (Sodium do

Re: [gmx-users] Questions about free energy calculation tutorial

? Thanks a lot! > On 28 Oct 2016, at 17:05, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 10/28/16 4:22 AM, gozde ergin wrote: >> Thanks Justin, >> >> Actually for my case I’ll put the methane molecule inside cubic box not >> spherica

Re: [gmx-users] Questions about free energy calculation tutorial

Ok thanks Justin! > On 28 Oct 2016, at 17:05, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 10/28/16 4:22 AM, gozde ergin wrote: >> Thanks Justin, >> >> Actually for my case I’ll put the methane molecule inside cubic box not >> spherica

Re: [gmx-users] Questions about free energy calculation tutorial

-bottom restraint energy, do you think I just need to remove these energy from the result \DeltaG? I would like to learn if you have any idea and source to suggest. Thanks in advance. > On 27 Oct 2016, at 20:58, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 10/27/16 11:35

[gmx-users] Questions about free energy calculation tutorial

Dear all, I follow the Justin’s free energy calculations: Methane in Water tutorial. (Thanks Justin!) I would like to ask two questions: 1) Is there specific reason to use sd integrator? 2) Methane molecules is free to sample every x,y,z point in the water bulk. I would like to apply a

[gmx-users] Partial charges correction from PRODRG

Dear all, Thanks to the Lemkul et.al. 2010 paper, we know that charges are often inconsistent in topologies produced by PRODRG. I have two types organic molecules to simulate, SDS and C12betaine. There are a lot of studies about SDS so I found the optimised charge distribution for Gromos-UA

Re: [gmx-users] Umbrella sampling tutorial

Any idea on this topic? Thanks > On 07 Oct 2016, at 14:13, gozde ergin <gozdeeer...@gmail.com> wrote: > > Thanks Justin. > I want infinite dilute bulk that’s why I do not want any surfactant molecule > inside the bulk. > I may put a ‘’wall’’ just below the surface molec

[gmx-users] Re-center the trajectory

Dear all, After 20 ns simulation I would like to re-center my trajectory according to the "centre of box” which is 2.4 2.4 15. I almost tried all trjconv options (-pbc with mol, -center, -ur compact) however the trajectory still moves the +z/-z direction. Is there any way to re-center the

Re: [gmx-users] Thermodynamic integration and re-weighting method

ted if you could let me also know how to use if you find out either > by this or ... . > > Best regards, > > Alex > > On Mon, Oct 17, 2016 at 6:14 PM, gozde ergin <gozdeeer...@gmail.com> wrote: > >> Any idea? >> Thanks. >>> On 13 Oct 2016, at 15:42, gozde e

Re: [gmx-users] Thermodynamic integration and re-weighting method

Any idea? Thanks. > On 13 Oct 2016, at 15:42, gozde ergin <gozdeeer...@gmail.com> wrote: > > Dear all, > > I will use Gromacs to calculate the chemical potential difference of > solvation a surfactant molecule on the surface. > System covers water molecules covere

[gmx-users] Thermodynamic integration and re-weighting method

Dear all, I will use Gromacs to calculate the chemical potential difference of solvation a surfactant molecule on the surface. System covers water molecules covered with surfactant molecules. I will apply flat-bottom restraint to the surfactant molecules in order to stabilise them on surface. I

Re: [gmx-users] Umbrella sampling tutorial

tin Lemkul <jalem...@vt.edu> wrote: > > > > On 10/7/16 4:41 AM, gozde ergin wrote: >> Dear all, >> >> I would like to ask a question about Justin’s tutorial. By using the >> POSRES_B, a restraint is applied on chain B in order to immobile it. Is the >&g

[gmx-users] Umbrella sampling tutorial

Dear all, I would like to ask a question about Justin’s tutorial. By using the POSRES_B, a restraint is applied on chain B in order to immobile it. Is the effect of this restraint removed during the WHAM? I want to do a similar thing by applying restraint force on the organic molecule on the

[gmx-users] Synergism with MD

Dear users, I would like ask a general question. I want to estimate the synergism in surface tension reduction effectiveness by using MD. There are experimental studies about this topic however I could not find a MD study. Do you aware any MD studies related the synergism in surface tension for

Re: [gmx-users] What is the meaning of negative surface tension?

Also when I check the pressure in X,Y and Z axis, Pzz = -0.34 bar Pyy = -1275 bar Pxx = 32 bar. Pyy and Pxx should be equal to each other. So basically system is not under equilibrium conditions. How should I solve this problem? Any idea? > On 23 Sep 2016, at 09:27, gozde ergin <go

[gmx-users] What is the meaning of negative surface tension?

Dear all, I am simulating organic covered salty water system in order to estimate the surface tension. Force field is Charmm36 and water model in TIP3P. Surface tension is -127 mN/m after 5 ns run. What is the meaning of negative surface tension? I was expecting +30 ~ +40 mN/m but not negative.

Re: [gmx-users] CHARMM-GUI files give error in Gromacs

Ok I will. Thank you very much Justin. > On 02 Sep 2016, at 16:58, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 9/2/16 10:44 AM, Justin Lemkul wrote: >> >> >> On 9/2/16 10:43 AM, gozde ergin wrote: >>> Ok I understand. I

Re: [gmx-users] CHARMM-GUI files give error in Gromacs

Ok I understand. I did exactly same thing for another molecule (SDS) and everything is working without any error. But I do not know what should I do with cis-pinonic. > On 02 Sep 2016, at 16:40, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 9/2/16 10:39 AM, gozde ergi

Re: [gmx-users] CHARMM-GUI files give error in Gromacs

Hi Justin, I try to use the CHARMM-GUI files directly. My purpose is simulating the water and ci-pinonic system. Cis-pionic molecules will stay on the water surface and I would like to estimate surface tension reduction. What should I change in CHARMM-GUI files? > > CHARMM-GUI provides a

[gmx-users] CHARMM-GUI files give error in Gromacs

Dear all, I used CHARMM-Gui and prepared the .pdb, .itp and .top file for cis pionic acid. After that I used genbox command of gromacs and add some water molecules. When I try to run I get 100 Errors saying : No default bond types, No default U-B types, No default Proper Dih. types, No default

Re: [gmx-users] Free energy calculation, Methane in water tutorial

The error is pretty clear. Do you produce the min0.tpr file? Where do you put this file? Is it in the same directory of job.sh file? > On 02 Sep 2016, at 13:09, Sun Iba wrote: > > Hello dear users > > I am following Justin's tutorial for free energy calculation of Methane

Re: [gmx-users] SHAKE error

No I am using same Gromacs 4.6.5. I run these two simulations again one runs and the other fails with the same .mdp file. > On 22 Jul 2016, at 13:53, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 7/22/16 7:50 AM, gozde ergin wrote: >> Dear all, >> &

[gmx-users] SHAKE error

Dear all, I use md-vv and SHAKE algorithm however I face an error which I was not before. Before I had 1-decanol and water system and now I have cis-pionic and water system. I exactly use the same .mdp file just as before however this error comes : SHAKE is not supported with domain

Re: [gmx-users] md-vv and md

Dear all, I am using md-vv integrator in 5.1 and still get this all bulk moving problem. Before I was using 4.6 and informed that this dribble is fixed 5.1 however I still got the same problem. My bulk is moving in z direction however if I use md integrator I do not face with this problem. Any

Re: [gmx-users] Average simulation time for correct surface tension

Maybe this is better https://imgur.com/hLFbjS8 <https://imgur.com/hLFbjS8> > On 18 Jul 2016, at 17:40, gozde ergin <gozdeeer...@gmail.com> wrote: > > Thanks Justin, > > Here is the plot for the average of 1ns chunks of time (with error) > > https://img

Re: [gmx-users] Average simulation time for correct surface tension

Thanks Justin, Here is the plot for the average of 1ns chunks of time (with error) https://imgur.com/FPmxysO <https://imgur.com/FPmxysO> It is hard to tell. > On 18 Jul 2016, at 16:18, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 7/18/16 10:16 AM,

Re: [gmx-users] Average simulation time for correct surface tension

not. Also this surface tension value is not correct either. It should be around 1000-1100 not 1244 bar nm. On 18 Jul 2016, at 16:06, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 7/18/16 6:07 AM, gozde ergin wrote: >> Dear users, >> >> I am trying to estimate the

[gmx-users] Average simulation time for correct surface tension

Dear users, I am trying to estimate the surface tension of cis-pinonic covered water surfaces. Li. et al 2010 did the same thing and his simulation time was 2 ns. On the other hand there are some other studies mentioned that simulation time should be long around 200 ns because surface tension

Re: [gmx-users] Surface tension calculation for organic monolayer

e lower than acids). >> I doubt this error coming from the pH effects. >> But how could i get the protonated molecules configuration? >>> On 07 Jul 2016, at 17:11, David van der Spoel <sp...@xray.bmc.uu.se> > wrote: >>> >>> On 07/07/16 16:06, gozde e

Re: [gmx-users] Surface tension calculation for organic monolayer

and estimated the reduced surface tension? Any suggestion would be really helpful. I tried some other force field (GAFF, AMBER, OPLSAA) but results did not change. I am doing something wrong but I do not know what. > On 07 Jul 2016, at 17:51, gozde ergin <gozdeeer...@gmail.com> wrote:

Re: [gmx-users] Restart corrupted run

> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations > It explains the restart procedure for version 4 and newer. > On 13 Jul 2016, at 12:01, Mehrnoosh Hazrati > wrote: > > Hi

Re: [gmx-users] Surface tension calculation for organic monolayer

:11, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > > On 07/07/16 16:06, gozde ergin wrote: >> Dear users, >> >> I simulated three different systems in cubic box and calculated their >> surface tension as shown below; >> >> 1. Pure water , surfac

[gmx-users] Surface tension calculation for organic monolayer

Dear users, I simulated three different systems in cubic box and calculated their surface tension as shown below; 1. Pure water , surface tension = 61.5 mN/m 2. Water with 3M NaCl salt, surface tension = 66.5 mN/m 3.Water surface covered with cis-pinonic organic, surface tension = 63.5 mN/m

Re: [gmx-users] Topology include file " " not found

Ok I found the error. I put “cis-pinonic.itp” instead of ”cis-pinonic.itp”. The problem is quote. On 26 Apr 2016, at 13:35, gozde ergin <gozdeeer...@gmail.com> wrote: > > I checked it and there is no #include statement in cis-pinonic.itp file. >> On 26 Apr 2016, at 13:24, Ju

Re: [gmx-users] Topology include file " " not found

I checked it and there is no #include statement in cis-pinonic.itp file. > On 26 Apr 2016, at 13:24, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 4/26/16 5:57 AM, gozde ergin wrote: >> Dear all, >> >> I am trying to simulate organic system. >>

[gmx-users] Topology include file " " not found

Dear all, I am trying to simulate organic system. Here is my tool.top file, and cis-pionic,its is in the same folder with the tool.top. ; ; Topology from .mol2 file ; topolbuild ; ; The force field files to be included #include "charmm27.ff/forcefield.itp" ; Include chain topologies #include

Re: [gmx-users] semi-permeable wall in gromacs

Is refcoord_scaling the issue for also NVT simulation? Because Roux and Luo did NVT after equilibrate the system in semiisoptropic NPT. > On 19 Apr 2016, at 14:06, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/19/16 6:15 AM, gozde ergin wrote: >> T

Re: [gmx-users] semi-permeable wall in gromacs

kul <jalem...@vt.edu> wrote: > > > > On 4/7/16 12:57 PM, gozde ergin wrote: >> Hi Justin, >> >> I just want to ask how is the r(nm) in posre.itp working? >> >> I would like to put semi-permeable wall on +/- 2.4 nm in z coordinate of the &g

Re: [gmx-users] Osmotic pressure

correction DispCorr= no > On 18 Apr 2016, at 15:48, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 4/18/16 4:43 AM, gozde ergin wrote: >> In Roux study they did 10 independent 1.5 ns production simulation and I did >> 15 ns simulation and d

Re: [gmx-users] Osmotic pressure

Hi Mark, I guess so because a lot of studies cite this study also their results are almost identical with the experimental one. > On 18 Apr 2016, at 10:46, Mark Abraham wrote: > > Are they known to produce these observables accurately -- Gromacs Users mailing list

Re: [gmx-users] Osmotic pressure

) Experiment 300 bar > On 18 Apr 2016, at 10:29, Mark Abraham <mark.j.abra...@gmail.com> wrote: > > Hi, > > What statistical error do you (and they) measure? How many replicates have > each of you done? > > Mark > > On Mon, 18 Apr 2016 10:25 gozde

Re: [gmx-users] Osmotic pressure

suggestions would be appreciated. > On 15 Apr 2016, at 11:50, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 4/15/16 5:20 AM, gozde ergin wrote: >> Dear all, >> >> I simulate the NaCl solution to estimate the osmotic pressure. My salt >> conce

Re: [gmx-users] position restrain energy

You defined in .top file as POSRES_Protein so in .mdp file you should call as define = -DPOSRES_Protein. The names in .top and .mdp should match On 18 Apr 2016, at 08:46, Nikhil Maroli wrote: > > Dear all, > i wanted to include position restrain to cyclic peptide

Re: [gmx-users] on force field for ligand

Hi Brett, If you have all the necessary .itp files and if your .top file is generated correctly, yes it works. > On 18 Apr 2016, at 09:23, Brett wrote: > > Dear All, > > > Does GROMACS work if the force field for ligand part is GAFF force field? > > > Brett > -- >

Re: [gmx-users] Osmotic pressure

> > On Fri, 15 Apr 2016 11:50 Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 4/15/16 5:20 AM, gozde ergin wrote: >>> Dear all, >>> >>> I simulate the NaCl solution to estimate the osmotic pressure. My salt >> concent

[gmx-users] Osmotic pressure

Dear all, I simulate the NaCl solution to estimate the osmotic pressure. My salt concentrations are 3,4 and 5M. I apply flat-bottom restraint to the molecules. I use CHARMM36 ff with NBFIX correction. After the simulation I extract the z-coordinates of restraint ions and use the equation P =

Re: [gmx-users] CHARMM36 ff with NBFIX in grimaces

Thanks Justin. In order to validate the results from Luo and Roux 2010 study, I need to run the simulations with and without NBFIX. But thank you very much for your respond, I appreciate it. > On 12 Apr 2016, at 13:25, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 4

[gmx-users] CHARMM36 ff with NBFIX in grimaces

Dear all, I try to simulate the salt solution by using charmm36 ff in gromacs. I downloaded charmm36.ff from MacKerell web page. forcefield.to file ; ; This force field generated by charmm2gmx.py from ; multiple charmm parameter files ; and multiple charmm topology files #define _FF_CHARMM

Re: [gmx-users] semi-permeable wall in gromacs

Yes it worked. I appreciated to your help Justin. Thanks a lot. > On 07 Apr 2016, at 21:37, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 4/7/16 12:57 PM, gozde ergin wrote: >> Hi Justin, >> >> I just want to ask how is the r(nm) in posre.itp w

Re: [gmx-users] semi-permeable wall in gromacs

restraint travel +/- 2.4 nm. But I do not want this, I would like to put a wall or force on +/-2.4 nm in z of the box. Do you have any advice about this? Thanks in advance. > On 21 Mar 2016, at 18:37, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 3/21/16 1:29 PM, goz

[gmx-users] Inorganic ammonium sulphate with CHARMM force field

Hi everybody, I would like o run ammonium sulphate solution with CHARMM force field in GROMACS. pdb2gmx is not working because the residue type is LIG. I tried to use swissparam and paramchem website however both do not support the inorganic sulphate and ammonium explicitly. Is there any other

Re: [gmx-users] semi-permeable wall in gromacs

Ok this was a silly question. In g_energy command 5. one is flat-bottom posres force. Sorry. > On 21 Mar 2016, at 17:26, gozde ergin <gozdeeer...@gmail.com> wrote: > > Hey Justin, > > I am just wondering in order to estimate the osmotic pressure I need extract > t

Re: [gmx-users] semi-permeable wall in gromacs

gt; wrote: > > > > On 3/10/16 4:44 AM, gozde ergin wrote: >> Dear Justin, >> >> Thanks for your respond, I assume there is a way to apply this restraint on >> specific molecules. >> Because my system is mixed with organic and water and I would like to ap

Re: [gmx-users] semi-permeable wall in gromacs

Dear Justin, Thanks for your respond, I assume there is a way to apply this restraint on specific molecules. Because my system is mixed with organic and water and I would like to apply these forces on organic molecules not water? > On 09 Mar 2016, at 18:30, Justin Lemkul

[gmx-users] semi-permeable wall in gromacs

Dear all, I would like to compute the osmotic pressure directly from all-atom MD simulations of concentrated aqueous solutions. The basic idea is to introduce “virtual” walls to represent the effect of ideal semipermeable membranes, separating a high concentration region from a pure water

[gmx-users] Thermal energy

Dear users, Is there way to extract the thermal energy of the system that simulated in NVT ensemble? thanks -- 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] Umbrella sampling and dividing the forces into mean force + friction force + random force

Maybe someone has an idea how to extract the instantaneous forces from the trajectory. I would normally use g_traj command to extract the forces however I am not sure if this force means instantaneous force. On Wed, Nov 25, 2015 at 2:02 PM, gozde ergin <gozdeeer...@gmail.com> wrote:

[gmx-users] Umbrella sampling force autocorrelation

Dear Gromacs user, I did umbrella sampling by pulling a water molecule from gas phase to organic coated bulk water. By clicking the link below you can see my PMF profile. In order to estimate the transmission coefficient, I put the pulled molecule on the top of the PMF barrier and did simulation

[gmx-users] Umbrella sampling and dividing the forces into mean force + friction force + random force

Dear gromacs users, I would like ask a question about the force of umbrella sampling. I did umbrella sampling by pulling a water molecule from gas phase to organic coated bulk water. I estimated the free energy profile on this reaction coordinate. In order to calculate the random force-force

Re: [gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem

n. > > Mark > > > On Thu, Nov 5, 2015 at 1:23 PM gozde ergin <gozdeeer...@gmail.com> wrote: > > > - system 512 water molecule covered by 25 organic on each surface, > > - I used both gromacs 4.5 and 5.0 with and without double precision > > - .mdp file is : &

Re: [gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem

ed for me. > > On Wed, Nov 4, 2015 at 2:47 PM, gozde ergin <gozdeeer...@gmail.com> wrote: > > > Dear Chaban, > > > > I decreased the time step and also I run by using double precision > however > > energy kept decreasing and did not converge. > &g

Re: [gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem

y not providing a readable .mdp > file, not specifying a GROMACS version, nor describing what is in your > system. If there was a magic "do this and energy is conserved" button then > it'd be already pushed for you ;-) > > Mark > > On Thu, Nov 5, 2015 at 11:34 AM gozde

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