[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 auto-

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

; Even with that fixed, the use of constraints intrinsically leads to drift, > also. Whether the remaining drift matters for your simulation (vs the > decrease in sampling you would have to accept in order to start to deal > with it) is an open research question. > > Mark > > >

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

dp > 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 ergin wrote: > > &

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

duce some of the parameters as follows > (keeping the rest same) - > > lincs_iter = 2 > rvdw-switch = 1.1 > vdwtype = Cut-off > vdw-modifier = Force-switch > > I recently faced some of the same problems as yours and the above > parameters worked for me. > > On Wed,

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

: > Decrease the time-step. > > > > > On Tue, Nov 3, 2015 at 3:00 PM, gozde ergin wrote: > > > -- Forwarded message -- > > From: gozde ergin > > Date: Tue, Nov 3, 2015 at 5:39 PM > > Subject: NVT to NVE ensemble, energy drifting problem &

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

-- Forwarded message -- From: gozde ergin Date: Tue, Nov 3, 2015 at 5:39 PM Subject: NVT to NVE ensemble, energy drifting problem To: mailing list Gromacs Dear Gromacs user, I did some simulation in NVT ensemble now I need to switch and do some more simulations in NVE ensemble

[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 kineti

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 t

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 wrote: > Hi Justin, > > It is totally random. My syste

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

, Oct 23, 2015 at 7:10 PM, Justin Lemkul 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 configurations on >> reaction &g

[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 equilibra

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

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 wrote: > On 06/10/15 12:08, gozde ergin wrote: > >> Thank you Mark but I could not understand how to do a 'suitably hacked >> .t

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

bly hacked .tpr to get what you want. > > Mark > > On Tue, Oct 6, 2015 at 11:34 AM gozde ergin wrote: > > > Dear users, > > > > Is there way to extract only van der Waals forces from trajectory in > > Gromacs 5.0? > > > > Thanks in advance >

[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 http://www.gromacs.org/Su

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

; 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, which likely can't even

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 wrote: > Dear gromacs users; > > I am trying to estimate the force-force auto correlation function. > To do that first I run the command of : > > &#x

[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 : 'g_analyze

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 t

[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] 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 sea

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 wrote: > Dear all,I am simulating polarizable water with Gromacs 5.0.5. I am > wondering if it is possible to calculate the pressure profiles along

[gmx-users] Surface roughness

Hi all, Is there a tool to calculate the surface roughness in Gromacs? I have five different organic surfaces run in NVT ensemble and I would like to estimate their roughness. Thanks in advance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing

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 wrote: > Dear users > > I'm trying to create a topology file for a molecule to oplsaa force f

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 wrote

[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 order

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 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

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

grator : md-vv)? And why I do not see the same jump by using md integrator? thanks in advance <http://imgur.com/6aJkRoQ&fjXGmXu#0> On Mon, Jun 22, 2015 at 6:22 PM, gozde ergin wrote: > Hi Michael, > > There is one more question, I still could not get why do I see that bi

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

But why? On Fri, Jul 17, 2015 at 6:07 PM, David van der Spoel 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 b

[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 , http://imgur.com/sFF

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 wrote: > > > On 7/16/15 12:26 PM, gozde ergin wrote: > >> Thank for reply

Re: [gmx-users] g_covar Segmentation fault problem

t; On 7/16/15 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 >

[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 (122

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

PM, gozde ergin wrote: > Thanks Michael. > > On Mon, Jun 22, 2015 at 3:50 PM, Michael Shirts > wrote: > >> At some point, a COM removal step was omitted for md-vv. A change has >> been >> proposed in in gerrit for a while (See >> https://ge

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

t 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 > wrote: > >

[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 ene

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 http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/rele

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 wrote: > Hi Mark, > > What do you mean by saying "thing"? Is phase ch

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 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

[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/l9mJesD,ggDDZtb#0 (first pic) I just could not understand what is going on after 7.5 ns? Also I am doing this simulation to calcul

[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 lin

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 wrote: > Hi all, > > I am simulating the organic-water system by using umbrella sampling method. > I w

[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 solvent

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 wrote: > > > On 6/6/15 2:57 PM, gozde ergin wrote: > >> Actually I know I need to do something

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

Actually I know I need to do something like this however I don't know how to do it. Could anybody give a hint how this approach can be realized in GROMACS? I could not find a clear answer in manual. On Thu, Jun 4, 2015 at 6:38 PM, Justin Lemkul wrote: > > > On 6/4/15 10:43 AM, goz

[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 --

Re: [gmx-users] Gas phase simulation

eed (though that > should not be a problem, just 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 > Se

Re: [gmx-users] Gas phase simulation

h.se/pipermail/gromacs.org_gmx-users/2015-April/096847.html > > but you don;t say what they are (or I missed it). > > Chris. > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.k

Re: [gmx-users] Gas phase simulation

e the solute is in the > organic phase and one image of an umbrella where the solute is in the gas > phase? > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf o

Re: [gmx-users] Gas phase simulation

urb the organic/air interface (and then there > is also no need for the initial NPT to evaluate average volume and also you > can do the US in NPT). > > > Nevertheless, the above is just one hack to force your system to behave as > you are asking it to. It's probably better to

[gmx-users] Fwd: Gas phase simulation

-- Forwarded message -- From: gozde ergin 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 system I am using Gromacs

[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 that

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