[gmx-users] Reg: Simulating large number of molecules

Hi all I want to simulate more than 1000 molecules of say octane r any alkanes in gromacs. after doing a little math i find my box dimensions for the molecules. but when i use genbox to insert multiple molecules in my local system after running some time it says cannot allocate memory but when the

[gmx-users] Reg: Dihedral conversion from fourier to RB form

Hi all I want to convert the fourier co-efficients into RB form.i have V1, V2 and V3 in the literature. My question is V1,V2 and V3 corresponds to F1,F2 and F3 in the manual?. I just want to confirm one more thing to convert fourier coefficients to RB form the formula i have to use is 4.64 in the

Re: [gmx-users] Reg: fatal error pdb2gmx

Even though the UA force field is outdated i want to use that and try to rectify the cryptic error message that keeps coming. Thank you very much for your suggestions Justin. Regards Vinoth On Mon, Dec 20, 2010 at 11:15 AM, Justin A. Lemkul wrote: > > > vinothkumar mohanakrish

Re: [gmx-users] Reg: fatal error pdb2gmx

Hi Justin I had taken United atom pdb file form PRODRG and i want to use OPLS-UA force field. i dont know what's wrong out there.I have done it befor for other molecules like DCE, CCL4 etc. Regards Vinoth On Mon, Dec 20, 2010 at 11:01 AM, Justin A. Lemkul wrote: > > &g

[gmx-users] Reg: fatal error pdb2gmx

Hi all I want to use pdb2gmx to generate hexane topology and hexane.gro file. i have added the atom name in .atp file and corresponding section in .rtp file. i have given below my .rtp entry [ DRG ] [ atoms ] CAA opls_966 0 1 CAF opls_966 0 1 CAB opls_967 0 2 CAC opls_967 0 2 CAD opl

[gmx-users] Reg; Surface tension of liquid-liquid interface

Hi all I had simulated water-ccl4 (ccl4-water-ccl4) interface and measured the interfacial tension in NVT ensemble and i found a average value to be 97.0615 mN/m (correct me if iam wrong) and divided it by two (because i had two surfaces) to get the interfacial tension of single liquid-liquid inte

Re: [gmx-users] water-air interface surface tension

Hi David Can you tell me which journal, volume and page number. I am not able to acess the link you have given. any help is highly appreciated Regards Vinoth 2010/12/9 David van der Spoel > On 2010-12-09 09.20, gromacs wrote: > >> Hi, experts, >> I'd like to calculate the surface tension at wa

Re: [gmx-users] Reg: Surface tension of water

inoth 2010/12/7 André Farias de Moura > did you increase the size of the box in one direction in order > to create a water/vacuum interface on each side of the water > slab? > best, > Andre > > On Tue, Dec 7, 2010 at 8:21 AM, vinothkumar mohanakrishnan > wrote: > > Hi

[gmx-users] Reg: Surface tension of water

Hi all I want to calculate the surface tension of water using SPC model of water. I searched the mailing list and there is no post on the surface tension of water.I performed md simulation of 482 molecules of water in a triclinic box. I got the average surface tension value of water (300K) as 38.3

Re: [gmx-users] Reg: Standard error

/12/2010 7:59 PM, vinothkumar mohanakrishnan wrote: > >> Hi Gromacians >> >> I am planning to compute the standard error for the interfacial surface >> tension of water-dichloro ethane. i just want to know is my procedure right. >> below is the result what i get from m

[gmx-users] Reg: Standard error

Hi Gromacians I am planning to compute the standard error for the interfacial surface tension of water-dichloro ethane. i just want to know is my procedure right. below is the result what i get from my g_energy command. Statistics over 51 steps [ 0. thru 1000.0001 ps ], 1 data sets All av

[gmx-users] Reg:Uncertainty in the average value

Hi all I calculated the surface tension of dce (dichloroethane) using the g_energy command and found the average surface tension value to be 30.68 mN/m. what i want to know is how to find the standard error or the uncertainty of the average value in gromacs? i know one should always report the val

[gmx-users] Reg: Interfacial tension

Hi all I want to calculate the interfacial tension of two immiscible liquids using the surface tension option in gromacs. when i do that i am getting the error message as "One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than

[gmx-users] Reg: Interfacial tension

Hi all How to find the interfacial tension between two immiscible liquids in gromacs?. how one should start abou it. any help is highly is appreciated. Regards Vinoth -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] Reg: Unit Of Surface Tension

Hi all What is the unit of Surface tension that one obtains from Gromacs using the g_energy command?. I searched the mailing list and i found two posts but the answers seems to be contradictory. Because in one post it was said that mN/m and in the other bar nm. below are the link of the two post.

[gmx-users] Reg: pcoupling and ref_p

Hi Gromacians I have created two liquid-liquid interfaces by combining three (DCE-Water-DCE) boxes. I want to calculate the Interfacial surface tension by using the surface tension option in Gromacs. I know that I need to give two values for ref_p one for xy and other for z. it was said in the man

[gmx-users] Reg: Surface tension ref_p

Hi all I have created two liquid-liquid interfaces by combining three (DCE-Water-DCE) boxes. I want to calculate the Interfacial surface tension by using the surface tension option in Gromacs. I know that I need to give two values for ref_p one for xy and other for z. it was said in the manual tha

[gmx-users] Reg:Density Profile

Hi all, I have a system composed of DCE and Water in a 2.17x2.17x4.9800 simulation box with an dce-water interface.I want to investigate the density profile of the system, and I used the following command line to do that: g_density -f traj.xtc -n index.ndx -dens number -sl 100 The density profi

Re: [gmx-users] error in editconf step

Hi try the below command. in your command you have _d in the editconf which is unnecessary. hope it works editconf -f K2496T.gro -o boxx.gro -bt cubic -d 0.5 Regards Vinoth On Tue, Nov 9, 2010 at 11:28 AM, priyam saxena wrote: > Hey everybody, > > Eveytime I use the editconf command, it gives

Re: [gmx-users] problem with g_density

Hi all I also faced a similar problem like Ozge Engi when i used the g_density command for water-DCE interface. when i saw the final .gro file in VMD i saw some 20-25 molecules of water came on one side (end of DCE side) of the box and few molecules of DCE say 5 molecules on the end of water side

[gmx-users] Reg:Usage of Walls

Hi all I have a question regarding the usage of walls. what for walls are used? what difference does the presence of walls make in the simulation? kindly me more specific (if possible explain it with an example). any help is highly appreciated. it will be of great use for all the new users of Grom

Re: [gmx-users] Reg:walls and pbc xy

Hi all Can anyone help me out with the wall settings for running above mentioned liquid-liquid interface. with the mdp file i have my system is exploding. any help is highly appreciated. Regards Vinoth On Tue, Nov 2, 2010 at 3:58 PM, vinothkumar mohanakrishnan < kmvin...@gmail.com> wrote:

Re: [gmx-users] Reg:walls and pbc xy

Hi Berk Thank you. what settings i should change in mdp file (energy minimisation) to run the energy minimisation for the single liquid-liquid interface (liquid-vapour interface at the other two extremes) without any issues? kindly be specific ( what parameter i should change) below is my mdp file

Re: [gmx-users] Reg:walls and pbc xy

Hi Berk Thank you once again. How can i use thick layers and what is the procedure? can you explain it bit more on this? Regards Vinoth On Tue, Nov 2, 2010 at 3:18 PM, Berk Hess wrote: > Hi, > > I have not heard about such issues, but it might depend a lot on your > particular application. >

Re: [gmx-users] Reg:walls and pbc xy

Hi Berk I need only one interface because if i have two interfaces the "capillary waves from one interface disturb the other even though the distance between the average positions of the two interfaces are larger than the potential cut-off" (this was said in the literature). Can anyone explain me

[gmx-users] Reg:walls and pbc xy

Hi Gromacians I want to create a liquid-liquid interface and study its properties. Hence i combined two boxes ( say water and DCE). The two boxes are well equilibrated before merging and i created an interface. Now i want to perform energy minimisation for the interface by appling pbc in the xy d

Re: [gmx-users] Reg: NPT Equilibration of water

Compressibility value of water. ( http://www.mail-archive.com/gmx-users@gromacs.org/msg01245.html) Regards Vinoth On Fri, Oct 29, 2010 at 4:42 PM, Justin A. Lemkul wrote: > > > vinothkumar mohanakrishnan wrote: > >> Hi Justin >> >> Thank you for your comments. Yes i want t

Re: [gmx-users] Reg: NPT Equilibration of water

i want to know ultimately is can i go ahead with this pressure ( i have no problem with temperature and density) for water to create an interface by combining two boxes? Regards Vinoth On Fri, Oct 29, 2010 at 4:21 PM, Justin A. Lemkul wrote: > > > vinothkumar mohanakrishnan wrote: >

Re: [gmx-users] Reg: NPT Equilibration of water

Vinoth On Fri, Oct 29, 2010 at 2:06 PM, Mark Abraham wrote: > On 29/10/2010 6:39 PM, vinothkumar mohanakrishnan wrote: > > I am using the semiisotropic pressure scaling because i want the box size > to remain the same as that of the original box size in X and Y axis and want > to

Re: [gmx-users] Reg: NPT Equilibration of water

-29 09.08, vinothkumar mohanakrishnan wrote: > >> >> Hi Mark >> >> I read the link before posting the question. even though the fluctation >> is between 500-600 (as said in the link) bar the average pressure is >> around 7.4 bar. my concern is the average pressure

Re: [gmx-users] Reg: NPT Equilibration of water

i want to avoid any complications there. Regards Vinoth On Fri, Oct 29, 2010 at 12:22 PM, Mark Abraham wrote: > On 29/10/2010 5:48 PM, vinothkumar mohanakrishnan wrote: > >> Hi Gromacians >> >> I want to do equilibration of water (spc model) first in the NVT ensembl

[gmx-users] Reg: NPT Equilibration of water

Hi Gromacians I want to do equilibration of water (spc model) first in the NVT ensemble and then in the NPT ensemble to maintain a temperature of 300K and a pressure of 1 bar respectively. The NVT equilibration works fine and the average temperature turns out to be 299.229 K. Energy

Re: [gmx-users] Reg; MD of DCE part II

Vinoth On Tue, Oct 26, 2010 at 4:34 PM, Justin A. Lemkul wrote: > > > vinothkumar mohanakrishnan wrote: > >> Hi Dallas / all >> >> I looked up at the pressure coupling section and i found how to keep the >> box size same for two axis and change only one ax

Re: [gmx-users] Reg; MD of DCE part II

Hi Dallas / all I looked up at the pressure coupling section and i found how to keep the box size same for two axis and change only one axis (i used semiisotropic pressure coupling type) but when i did that the average pressure i get after the run is negative where as i want it be close to 1 bar?.

[gmx-users] Reg:Pressure coupling not enough values (I need 2)

Hi all I want to equilibrate DCE molecules(108) in the NPT ensemble. the pressure coupling iam using semiisotropic coupling. i found a similar question in the archive but the links in that was not active ( http://www.mail-archive.com/gmx-users@gromacs.org/msg22160.html) i know i need to give two v

[gmx-users] Reg:Using Trjconv to combine two gro r pdb files

Hi gromacians I want to know how in the methanol-water tutorial ( http://manual.gromacs.org/current/online/mixed.html) they generated mixed.pdb or conf.gro (usr/local/gromacs/share/gromacs/tutor/mixed) using trjconv? any help is highly appreciated. Regards Vinoth -- gmx-users mailing listgmx

Re: [gmx-users] Reg; MD of DCE part II

change. what one will do if one wants to do in the NPT ensemble and wants to control the box dimensions? Regards Vinoth On Mon, Oct 25, 2010 at 12:15 PM, Mark Abraham wrote: > > > - Original Message - > From: vinothkumar mohanakrishnan > Date: Monday, October 25, 2010 15:57

[gmx-users] Reg; MD of DCE part II

Hi gromacians I performed md simulation of 108 dichloroethane molecules in isothermal-isobaric ensemble with the box size 3.002*2.17*2.17. after the simulation my box size has changed considerably from the initial size to 2.87882 2.08095 2.08095.why this happens? my second question is can i have

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

( red line) and plot?. does i need any command to get the running average?. any help is highly appreciated. Regards Vinoth On Thu, Oct 21, 2010 at 4:56 PM, Justin A. Lemkul wrote: > > > vinothkumar mohanakrishnan wrote: > >> Hi justin >> >> I found what went wrong and i

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

do that for DCE. any help is highly appreciated. Regards Vinoth On Wed, Oct 20, 2010 at 5:33 PM, Justin A. Lemkul wrote: > > > vinothkumar mohanakrishnan wrote: > >> Hi Justin >> >> I corrected the mistake what you said and i am able to run energy >> minimi

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

to the required temperature (300K) i found that the variation in the temperature was 100K (plus r minus) . i am not able find out what went wrong. any help is highly appreciated. Regards Vinoth On Mon, Oct 18, 2010 at 6:09 PM, Justin A. Lemkul wrote: > > > vinothkumar mohanakrish

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

should i need to add these parameters to the source directory ( usr/local/gromacs/share/gromacs/top)? Regards Vinoth On Mon, Oct 18, 2010 at 5:27 PM, Justin A. Lemkul wrote: > > > vinothkumar mohanakrishnan wrote: > >> Hi all >> >> i added new atomtype for dich

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

bond_atomtype CLAA Regards Vinoth On Mon, Oct 18, 2010 at 5:12 PM, Mark Abraham wrote: > On 18/10/2010 10:31 PM, vinothkumar mohanakrishnan wrote: > > Hi all > > i added new atomtype for dichloroethane (DCE) and added the corresponding > parameters in the .rtp, .atp, .bon.itp, .n

[gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

Hi all i added new atomtype for dichloroethane (DCE) and added the corresponding parameters in the .rtp, .atp, .bon.itp, .nb.itp respectively. given below are my additions to the corresponding files respectively. *ffoplsaa.rtp* [ DCE ] [ atoms ] CLAA opls_967 -0.2270 1 CAB opls_966 0.2270

Re: [gmx-users] Reg: Installing gromacs in cygwin

us make[3]: *** [grompp.exe] Error 1 make[3]: Leaving directory `/cygdrive/c/Packages/gromacs-4.0.5/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/cygdrive/c/Packages/gromacs-4.0.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/cygdrive/c/Packages/gro

Re: [gmx-users] Reg: Installing gromacs in cygwin

Its not clear to me what you are asking. if iam right the above message is the configure command that i used during installation of gromacs. Regards Vinoth On Mon, Oct 11, 2010 at 12:03 PM, Mark Abraham wrote: > > > - Original Message - > From: vinothkumar mohanakrishnan &g

Re: [gmx-users] Reg: Installing gromacs in cygwin

Hi mark I have installed cygwin 1.7.7(the latest version) and i want to install only gromacs 4.0.5 (for scientific continuity).any help is highly appreciated. Regards Vinoth On Mon, Oct 11, 2010 at 11:20 AM, Mark Abraham wrote: > > > - Original Message - > From:

[gmx-users] Reg: Installing gromacs in cygwin

Hi I am installing gromacs-4.0.5 in windows using cygwin and i followed th procedure described in the link http://lists.gromacs.org/pipermail/gmx-users/2009-September/044792.html. there is no problem with fftw-3.2.2 installation. while insatlling gromacs at first i gave the command (as said in the

Re: [gmx-users] How can I best setup the nodes number

I think the PME mesh part is ok and it should be less than 0.5 always. Regarding the nodes ask your administrator how many ppn one node have. example suppose if one node has 6 ppn then 12 nodes will have 72ppn which is sufficient to run md. hope the above explanation helps you. Regards Vinoth O

Re: [gmx-users] Reg: Energy minimisation of hexane

: > > > - Original Message - > From: vinothkumar mohanakrishnan > Date: Wednesday, October 6, 2010 15:20 > Subject: [gmx-users] Reg: Energy minimisation of hexane > To: Discussion list for GROMACS users > > > Hi all > > > > I am trying to simulate

[gmx-users] Reg: Energy minimisation of hexane

Hi all I am trying to simulate 150 molecules of hexane in a triclinic box (8.319*3.01*3.01 nm^3) using OPLSAA force field.I got the .gro file from PRODRG and generated the topology using X2top command. when i run energy minimisation for hexane my potential energy is positve. is this right?. what i

Re: [gmx-users] Reg:Equilibration

the potential energy and find out > the deviation in the energy if the deviation in the energy is within 10% > then ur equilibration is successful... > > On 5 October 2010 14:56, vinothkumar mohanakrishnan wrote: > >> Hi all >> >> Suppose say i have a box of decane

[gmx-users] Reg:Equilibration

Hi all Suppose say i have a box of decane molecules and i want to equilibrate. say i have all the necessary files to run mdrun. on what basis i say whether my equilibration is successful r not after the mdrun. what properties i should measure to know whether my equilibration was successful. Regar

Re: [gmx-users] Reg: Prodrg topology

s.org/index.php?title=Download_%26_Installation/Related_Software/MKTOP > > Mark > > - Original Message - > From: vinothkumar mohanakrishnan > Date: Tuesday, October 5, 2010 16:43 > Subject: [gmx-users] Reg: Prodrg topology > To: Discussion list for GROMACS users > > >

[gmx-users] Reg: Prodrg topology

Hi all I want to generate a topology file for say decane from prodrg for oplsaa force field. is it possible?. i get a topology file from prodrg for gromos96.1 force field and i am able to process it further. when i use the topology file generated for gromos96.1(from prodrg) for oplsaa i get the er

Re: [gmx-users] Reg: Putting molecules on one side of the box

box to > fill the rest with water. Cunning use of genconf should allow you to select > where the division lies. > > Mark > > > - Original Message - > From: vinothkumar mohanakrishnan > Date: Friday, September 24, 2010 17:22 > Subject: [gmx-users] Reg: Putting m

Re: [gmx-users] Reg: Putting molecules on one side of the box

lease do ask a focussed question on the list if you run into problems. > > Good luck! > > > Mark > > - Original Message - > From: vinothkumar mohanakrishnan > Date: Monday, October 4, 2010 21:58 > Subject: Re: [gmx-users] Reg: Putting molecules on one side of t

Re: [gmx-users] Reg: Liquid-liquid interface simulation

why don't someone can post the tutorial in the gromacs website? because gromacs was heavily used for liquid-liquid interface simulation.I hope probably i will do it in the near future. Regards Vinoth On Tue, Sep 28, 2010 at 4:05 PM, Justin A. Lemkul wrote: > > > vinothkumar

Re: [gmx-users] Reg: Liquid-liquid interface simulation

Is there any tutorial for liquid-liquid interface in any of the website?. Regards Vinoth On Tue, Sep 28, 2010 at 2:01 PM, David van der Spoel wrote: > On 2010-09-28 09.58, vinothkumar mohanakrishnan wrote: > >> Hi all >> >> Is that any one have liquid-liquid interface s

[gmx-users] Reg: Liquid-liquid interface simulation

Hi all Is that any one have liquid-liquid interface simulation (like lysozyme by justin). if so kindly share it through this discussiion forum.it will be of great help for the newusers like me to use gromacs for liquid-liquid interface simulation. Regards Vinoth -- gmx-users mailing listgmx-

Re: [gmx-users] Reg: Adding multiple molecules

Hi Justin Thank you for your suggestion. Regards Vinoth On Mon, Sep 27, 2010 at 4:52 PM, Justin A. Lemkul wrote: > > > vinothkumar mohanakrishnan wrote: > >> Hi justin >> >> if genbox is not able to find sufficient space then why should one >> calcul

Re: [gmx-users] Reg: Adding multiple molecules

command. everytime i need to update it manually.is there a way to update it automatically? Regards Vinoth On Mon, Sep 27, 2010 at 4:31 PM, Justin A. Lemkul wrote: > > > vinothkumar mohanakrishnan wrote: > >> Hi all >> >> I have a diffculty in adding multiple molecules

[gmx-users] Reg: Adding multiple molecules

Hi all I have a diffculty in adding multiple molecules of hexane to my box. my box size is 4.72*2.36*2.36 (nm) according to my number density calculations the box should fit 124 molecules of hexane whereas it adds only 76 molecules to the box below is my command. i had evev tried with -try command

[gmx-users] Reg: Putting molecules on one side of the box

Hi all I have a triclinic box of length of 8*3*3 nm. i want to put water on one side of the box and say decane on the other side of the box. How to generate .gro for the water-decane mixture such that they form two distinct parts of the box. Regards Vinoth -- gmx-users mailing listgmx-users@

Re: [gmx-users] Re: Reg: Gromacs binary liquid-liquid simulation

047 1.232 1DRG CAF 17 1.179 0.186 1.380 1DRG HAM 18 1.149 0.284 1.418 1DRG HAN 19 1.281 0.191 1.342 1DRG HAL 20 1.168 0.108 1.456 0.84818 0.84818 0.84818 Regards Vinoth On Mon, Sep 13, 2010 at 4:26 PM, Justin A. Lemkul wrote: > &g

[gmx-users] Reg: Gromacs binary liquid-liquid simulation

i want to do MD for hexane-water system. I got hexane.gro and hexane..itp from PRODRG 2.5 Beta server with that i made the hexane.top file. below is the serious of commands i executed in gromacs, i am adding 200 hexane molecules an 1115 water molecules. after the first genbox i checked my topolgy f