[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

[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

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

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

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

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

[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] 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

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

[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] 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] 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

[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

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

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] 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

[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] 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: > >

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

[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] 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 >

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

[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] 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

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

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

[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] 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

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

[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] 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] 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

[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 *

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] 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] 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

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

[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] 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 >

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

[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] 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

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] 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

[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

[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

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 &

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

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

; 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 > > >

[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 For

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

:11, David van der Spoel 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 , surface tension = 61.5 mN/m &

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 all, > > how can I restart a MD

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 wrote: > > Dear Spoel, > Tha

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

that did the MD simulations with surface active > molecules on water 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 kn

[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 is

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

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 wrote: > > > > On 7/18/16 6:07 AM, gozde ergin wrote: >> Dear users, >> >> I am trying to estimate the surface tension of

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 wrote: > > > > On 7/18/16 10:16 AM, gozde ergin wrote: >> S

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 wrote: > > Thanks Justin, > > Here is the plot for the average of 1ns chunks of time (with error) > > https://imgur.com/FPmxysO <https://imgu

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 i

[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 decomposit

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 wrote: > > > > On 7/22/16 7:50 AM, gozde ergin wrote: >> Dear all, >> >> I use md-vv and

Re: [gmx-users] SHAKE error

Yes this could be the reason. Thanks Justin. > On 22 Jul 2016, at 14:00, Justin Lemkul wrote: > > > > On 7/22/16 7:59 AM, gozde ergin wrote: >> No I am using same Gromacs 4.6.5. >> I run these two simulations again one runs and the other fails with the same >&

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 in > water. I have dow

[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 self

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 wrote: > > > > On 9/2/16 10:39 AM, gozde ergin wrote: >> Hi Ju

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 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 did exactly same thing for another mo

[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 wrote: >

[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

[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 b

Re: [gmx-users] Umbrella sampling tutorial

tin Lemkul 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 >> effect of this restr

[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

[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] Thermodynamic integration and re-weighting method

Any idea? Thanks. > On 13 Oct 2016, at 15:42, gozde ergin 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 covered with surfactant molecules

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

e if you find out either > by this or ... . > > Best regards, > > Alex > > On Mon, Oct 17, 2016 at 6:14 PM, gozde ergin wrote: > >> Any idea? >> Thanks. >>> On 13 Oct 2016, at 15:42, gozde ergin wrote: >>> >>> Dear all, >

[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 molecu

Re: [gmx-users] Umbrella sampling tutorial

Any idea on this topic? Thanks > On 07 Oct 2016, at 14:13, gozde ergin 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 molecules in order to inhibit >

[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 forc

[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 fla

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

flat-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 wrote: > > > > On 10/27/16 11:35 AM, gozde ergi

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

Ok thanks Justin! > On 28 Oct 2016, at 17:05, Justin Lemkul 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 >> spherical. > > The geometry of

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

? Thanks a lot! > On 28 Oct 2016, at 17:05, Justin Lemkul 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 >> spherical. > > The geometry of

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

anks in advance. > On 01 Nov 2016, at 13:21, Justin Lemkul 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 dodecyl sulfa

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

ecoupling, is it wrong? > On 02 Nov 2016, at 12:42, Justin Lemkul 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 be due to any number

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 wrote: > > > > On 11/3/16 10:56 AM, gozde ergin wrote: >>> You can decouple atomic and mo

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 topology you posted

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 und

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 separat

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 series

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 wrote: > > > > On 11/6/16 10:44 AM, gozde ergin wrote: >> >>> This may be unstable, and is generally not done. Turn off charges >>> linearly, then

[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. Actu

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 run pulling simulation for

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 wrote: > > > > On 11/6/16 8:27 AM, gozde ergin wrote: >> >>> I

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 wrote: > > Hi all, > > I tried to estimate the free energy of betaine on betaine covered surface. My > targe

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 > > > > the error was > > > G

Re: [gmx-users] Position restraints umbrella sampling

Maybe you should visit the manual for your last questions. In my paper I have also followed the Justin’s tutorial however I did not use restraint because for my purpose it was unnecessary. Justin used it because restraining one peptide makes the remaining four peptides more stable. > On 13 Jan

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 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List be

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 wrote:

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