[gmx-users] Fwd: Gas phase simulation

-- Forwarded message -- From: gozde ergin gozdeeer...@gmail.com Date: Wed, Apr 22, 2015 at 12:21 PM Subject: Gas phase simulation To: gromacs.org_gmx-users@maillist.sys.kth.se Dear Gromacs users, In order to estimate the free energy profile of water on organic coated-water

[gmx-users] Gas phase simulation

Dear Gromacs users, In order to estimate the free energy profile of water on organic coated-water system I am using Gromacs umbrella option. I put my water molecule far away from the bulk organic+water system and pulled this molecule through the bulk. When I checked the PMF profile I realized

Re: [gmx-users] Gas phase simulation

are asking it to. It's probably better to figure out i) if it is behaving physically realistically and ii) if not then why not (i.e., adjust the parameters). Chris. From: gozde ergin gozdeeer...@gmail.com Sent: 05 May 2015 07:16 To: Christopher Neale Subject: Fwd

Re: [gmx-users] Gas phase simulation

an inefficiency). Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of gozde ergin gozdeeer...@gmail.com Sent: 06 May 2015 10:23 To: gmx-us...@gromacs.org Subject: Re: [gmx-users

Re: [gmx-users] All bulk is moving during Umbrella sampling

Justin, thank you for the advice. But if I apply a force to keep molecules within a layer, how I will extract this force effect on PMF? On Sun, Jun 7, 2015 at 3:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/6/15 2:57 PM, gozde ergin wrote: Actually I know I need to do something like

[gmx-users] All bulk is moving during Umbrella sampling

Hi all, I am doing some umbrella sampling simulation in order to estimate the PMF profile of the system. While doing this simulations I did: -- Simulated the system in x*y*z box. -- In order to have a gas phase I expanded the z coordinate to 5z and simulate the system in x*y*5z -- Minimization

[gmx-users] md-vv and md

Hi all, I was using md-vv as an integrator however I discovered that all bulk was moving (drifting) during the simulation. Than I changed the integrator and used md. The bulk molecules did not move during the simulation, just stayed in the middle of box. I attached the potential and kinetic

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

/ ), but one of the developers asked to have the source of the problem traced to understand better what happened and fixed at that point and merged forward. Hopefully this can get sorted out later this week. On Mon, Jun 22, 2015 at 9:10 AM, gozde ergin gozdeeer...@gmail.com wrote: Hi all, I

Re: [gmx-users] energy groups definition

Ok! I solved the problem. Basically it is possible to write the name of two groups for energygroups that is written in index file. On Thu, Jun 11, 2015 at 10:28 AM, gozde ergin gozdeeer...@gmail.com wrote: Hi all, I am simulating the organic-water system by using umbrella sampling method. I

[gmx-users] Potential Energy-Umbrella sampling

Hi all, My system has 560 water molecules covered by 50 organic molecules. I run the simulation for 20 ns and here is my potential energy figure. http://imgur.com/DrBvnjs I just could not understand what is going on after 7.5 ns? Also I am doing this simulation to calculate the PMF. On the

Re: [gmx-users] Potential Energy-Umbrella sampling

it is not easy to capture what is going on there. On Mon, Jun 15, 2015 at 5:58 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Your trajectory went from one thing to a completely different thing, so what did your visual inspection of the trajectory tell you? Mark On Mon, 15 Jun 2015 17:54 gozde

Re: [gmx-users] Surface tension calculation and counting number of interfacial molecules

Actually you can check both density and surface tension values to understand if it is bulk or interface. To calculate the surface tension as a function of Z, I can suggest you to use Gromacs_LP gromacs source code (which you can download from

Re: [gmx-users] Potential Energy-Umbrella sampling

I am using md-vv as an integrator but if I use m , I don't see this drift (movement) in my system. This is also another problem that I could not figure out. On Mon, Jun 15, 2015 at 6:04 PM, gozde ergin gozdeeer...@gmail.com wrote: Hi Mark, What do you mean by saying thing? Is phase changing

[gmx-users] energy groups definition

Hi all, I am simulating the organic-water system by using umbrella sampling method. I would like to extract the solute-solvent and solvent-solvent interactions information from energy file. In order to do that I need to define energy groups in .mdp file. My solute is one water molecule and

[gmx-users] Umbrella sampling and transmission coefficient

Dear user, I did umbrella sampling simulation and get PMF profile of my system. In order to calculate the rate constant I need to estimate the transmission coefficient. Do you have any advice about getting the transmission coefficient in GROMACS? Best -- Gromacs Users mailing list * Please

Re: [gmx-users] Local pressure of water

Please check the link below, http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure On Tue, Aug 11, 2015 at 11:16 PM, 折晓会 shex...@hotmail.com wrote: Dear all,I am simulating polarizable water with Gromacs 5.0.5. I am wondering if it is possible to calculate the

[gmx-users] g_covar Segmentation fault problem

Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix

Re: [gmx-users] g_covar Segmentation fault problem

Ok by using version 4.6.6 I got this segmentation fault error which means number of frames should be equal or bigger than the number of degrees of freedom. On Thu, Jul 16, 2015 at 7:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 12:26 PM, gozde ergin wrote: Thank for reply Justin

Re: [gmx-users] g_covar Segmentation fault problem

/16/15 10:22 AM, gozde ergin wrote: Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3

[gmx-users] Umbrella sampling - decomposing of free energy

Dear gromacs users, I did umbrella sampling in order to estimate the PMF profile of my system. My system has 512 water molecules covered by 25 decanol molecules on both side. I pulled a water molecule bulk water to organic layer and than gas phase. (Please see the system pic ,

Re: [gmx-users] Umbrella sampling - decomposing of free energy

But why? On Fri, Jul 17, 2015 at 6:07 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 17/07/15 17:54, gozde ergin wrote: Dear gromacs users, I did umbrella sampling in order to estimate the PMF profile of my system. My system has 512 water molecules covered by 25 decanol molecules

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

)? And why I do not see the same jump by using md integrator? thanks in advance http://imgur.com/6aJkRoQfjXGmXu#0 On Mon, Jun 22, 2015 at 6:22 PM, gozde ergin gozdeeer...@gmail.com wrote: Hi Michael, There is one more question, I still could not get why do I see that big jump in potential energy

Re: [gmx-users] Umbrella sampling - decomposing of free energy

Thank you very much for your responds. I will run longer simulations. On Sat, Jul 18, 2015 at 9:17 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 17/07/15 18:11, gozde ergin wrote: But why? Larger fluctuations I guess. People find this in other packages too so it is a physical

[gmx-users] Umbrella sampling - abnormal potential energy profile and wrong PMF profile

Dear gromacs users, My simulation system has 512 water molecules covered by 25 organic molecules on each side (1st pic). I have also gas phase. Link for the plots : http://imgur.com/HobCa8H,shH3pA9,OZpCUTZ,DeDk35Q,iFDGzXW,67SHwUw,Jj572Wx,2E1TJuH,xNC3D1s,JChHqjO,Z5Uu1l1,2mKA8UO,9DSe8OO#0 In

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

Please check my last e-mail I gave some more information about my system and energy results. Here is the link for plots http://imgur.com/HobCa8H,shH3pA9,OZpCUTZ,DeDk35Q,iFDGzXW,67SHwUw,Jj572Wx,2E1TJuH,xNC3D1s,JChHqjO,Z5Uu1l1,2mKA8UO,9DSe8OO#2 On Sat, Jul 18, 2015 at 4:13 AM, Michael Shirts

Re: [gmx-users] Create file topology in oplsaa

Gromacs has OPLSAA force field. You can use pdb2gmx command. Also you can use topolbuild software. If you google it, you can easily find how to use it. On Tue, Jul 21, 2015 at 2:38 PM, Daniele Veclani danielevecl...@gmail.com wrote: Dear users I'm trying to create a topology file for a

Re: [gmx-users] Segmentation fault in some windows of umbrella sampling

, Oct 23, 2015 at 7:10 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/23/15 11:38 AM, gozde ergin wrote: > >> Dear users, >> >> I am doing umbrella sampling and using gromacs 4.6. >> I followed the Justin tutorial and generated 200 configuration

Re: [gmx-users] Segmentation fault in some windows of umbrella sampling

Also I tried the run these windows by using different computers and different Gromacs versions (5.0 and 5.1) however I always got the same segmentation fault error. On Sat, Oct 24, 2015 at 6:37 PM, gozde ergin <gozdeeer...@gmail.com> wrote: > Hi Justin, > > It is totally random.

[gmx-users] Segmentation fault in some windows of umbrella sampling

Dear users, I am doing umbrella sampling and using gromacs 4.6. I followed the Justin tutorial and generated 200 configurations on reaction coordinate. I faced segmentation fault error for 34 configurations (windows) but 166 of them run without any error. I thought maybe systems were not

Re: [gmx-users] 5ns simulation in 2 hours

I run 20ns simulation in 3.5hours and I assumed it is correct. My system size is 2.5x2.5x12.5nm with 512 water and 50 organics molecules. I do not use GPU. On Thu, Oct 29, 2015 at 2:04 PM, Jorge Fernandez-de-Cossio-Diaz < j.cossio.d...@gmail.com> wrote: > Also check your time step size. A large

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

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

cha...@gmail.com> wrote: > Decrease the time-step. > > > > > On Tue, Nov 3, 2015 at 3:00 PM, gozde ergin <gozdeeer...@gmail.com> wrote: > > > -- Forwarded message -- > > From: gozde ergin <gozdeeer...@gmail.com> > > Date: Tue, Nov 3,

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 : &

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

Dear Gromacs user, I did some simulation in NVT ensemble now I need to switch and do some more simulations in NVE ensemble. What properties do I need to change in .mdp file to get a good energy conversion? I used the same properties like NVT without temperature coupling but my potential and

[gmx-users] Van der Waals force extraction in Gromacs 5.0

Dear users, Is there way to extract only van der Waals forces from trajectory in Gromacs 5.0? Thanks in advance -- 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] autocorrelation function

I am trying to estimate the autocorrelation of force. To do that I need the get the time series of *the total bath force acting on a molecule and this molecule is the pulled molecule that I use for umbrella sampling*. What is the difference between total bath force acting on a molecule and sum of

[gmx-users] force-force correlation function

Hi all, Is there way to estimate the force-force correlation function in gromacs? bests -- 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] g_traj + g_analyze and core dumped error

Dear gromacs users; I am trying to estimate the force-force auto correlation function. To do that first I run the command of : 'g_traj -f tra.trr -s topol.tpr -of force.xvg' My force.xvg file covers for all atoms in simulation box which I have 9566 atoms. Than I run the command of :

Re: [gmx-users] g_traj + g_analyze and core dumped error

Also I did the same calculation for only one atom and did not get any error. On Wed, Sep 16, 2015 at 4:39 PM, gozde ergin <gozdeeer...@gmail.com> wrote: > Dear gromacs users; > > I am trying to estimate the force-force auto correlation function. > To do that first

Re: [gmx-users] g_traj + g_analyze and core dumped error

edu> wrote: > > > On 9/16/15 11:48 AM, gozde ergin wrote: > >> Also I did the same calculation for only one atom and did not get any >> error. >> >> >> > Probably because your original command will have 3*9566 floating-point > entries per line,

Re: [gmx-users] Van der Waals force extraction in Gromacs 5.0

the branching effect on the system I would like to extract van der waals forces of each system.. On Tue, Oct 6, 2015 at 1:32 PM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > On 06/10/15 12:08, gozde ergin wrote: > >> Thank you Mark but I could not understand how to do a 'suita

[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] 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] 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

[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

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

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

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

[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] 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] 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

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

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] 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] 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] 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] 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] 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] 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] 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

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] 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] 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] 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

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

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

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] 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:

[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

[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] 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] 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] 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, >> &

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_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

[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] 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

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

[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] 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

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] 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

[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] 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] 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] 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] 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

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

> 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

> 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

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

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