[gmx-users] reg pulling

Dear justin , Thank you for your nice reply. i am doing steered MD can i pulll the bonded atom ? by Keeping one atom reference and pulling other atom which is having bond with reference atom? otherwise  is pull  possible only between non bonded groups? Thanks  in advance --

Re: [gmx-users] How to recenter solvent around solute

Hi, Justin is very right to point at the workflow. In your case, the points 5 and 6 apply: centering, and putting things in some box. Maybe that doesn't work in one pass and you'll have to use trjconv twice. This does not work. Neither is the solute always surrounded by solvent for every frame

[gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0

Dear GMX-users, in a first trial, I successfully managed to compile gromacs 4.5.4 and fftw 3.2.2 by following the installation instructions on the gromacs main page. For these compilation, I did not specify the CC CXX or F77 (Compilation was accomplished by GNU compiler 4.5). I was forced to use

Re: [gmx-users] Umberella sampling

mohsen ramezanpour wrote: Dear Dr.Justin Regarding doing umbrella sampling: I used gen_vel =no and I prefer to use from thermodynamics of system in NPT.cpt Although the T and P were as I did set in NPT.mdp file (T=310 ,P=1 bar) But their values in my umbrela.log files are not as before

Re: [gmx-users] reg pulling

vidhya sankar wrote: Dear justin , Thank you for your nice reply. i am doing steered MD can i pulll the bonded atom ? by Keeping one atom reference and pulling other atom which is having bond with reference atom? otherwise is pull possible only between non bonded

Re: [gmx-users] Umberella sampling

Dear Dr.Justin I didn't any equilibration for any windows! Because: As I know the thermodynamics of the system had wroten in NPT.cpt file (for example the velocities and etc). Then when I use that in grompp for each windows ,I expect the same characteristics of system as before(At least the

Re: [gmx-users] ambar to opls force field

Thanks Justin. I am using flexibale water model for my system. I am refering a paper J. Chem. Phys. 124, 024503 (2006). Author have used Amber type force field. i.e. 1/2 Kbond (r-req)**2 + 1/2 Kangle(theta-thetaeq)**2. Kbond = 443153.3808 kJ/mol nm**2 Kangle= 317.5656 kJ/mol rad**2. I am

Re: [gmx-users] Umberella sampling

mohsen ramezanpour wrote: Dear Dr.Justin I didn't any equilibration for any windows! Because: As I know the thermodynamics of the system had wroten in NPT.cpt file (for example the velocities and etc). Then where does NPT.cpt come from? Presumably, if you have this file, you did some

[gmx-users] beware gen-vel=no

Regarding gen-vel=no as discussed here: http://lists.gromacs.org/pipermail/gmx-users/2011-May/061151.html I would caution against the general use of gen-vel=no and then coupling to a temperature of 300 K with the Berendsen thermostat. One problem that can arise is concerted unfolding.

Re: [gmx-users] Umberella sampling

Dear Dr.Justin Thank you for your complete explanation. Please let me discribe where is NPT.cpt comes from: Before doing Pulling step,I did an NPT step (as your tutorial) to generate NPT ensemble. the outputs of this step were NPT.cpt, NPT.gro and NPT.enr and ... Then I used NPT.gro for

Re: [gmx-users] Umberella sampling

mohsen ramezanpour wrote: Dear Dr.Justin Thank you for your complete explanation. Please let me discribe where is NPT.cpt comes from: Before doing Pulling step,I did an NPT step (as your tutorial) to generate NPT ensemble. the outputs of this step were NPT.cpt, NPT.gro and NPT.enr and

[gmx-users] about pullinng in steered MD

Dear justin  very thanks for your immediate reply,       During Steered MD i want to push some groups which is near to my reference Group  Which option can i use to push my mobile group towards reference group ? Thanks in advance -- gmx-users mailing list

Re: [gmx-users] about pullinng in steered MD

vidhya sankar wrote: Dear justin very thanks for your immediate reply, During Steered MD i want to push some groups which is near to my reference Group Which option can i use to push my mobile group towards reference group ? Set a pull_rate 0. -Justin --

Re: [gmx-users] trjconv center on protein

Dear Tsjerk, I was afraid that it works like this... It is possible to center the system in a different way? without this additional component to the water displacement? What I want is to have protein always in the center of my view But not by some artificial centering inside the box nor changing

[gmx-users] sphere around a protein

Hi Justin and other gmx-users, I want to make a sphere around a protein (5nm).with Li ions and anions. Justin, as you had suggested to use genbox -shell option, I tried using it but i realized that since my protein is a long tube like structure, the shell option generated a cyclinder around the

Re: [gmx-users] sphere around a protein

shivangi nangia wrote: Hi Justin and other gmx-users, I want to make a sphere around a protein (5nm).with Li ions and anions. Justin, as you had suggested to use genbox -shell option, I tried using it but i realized that since my protein is a long tube like structure, the shell option

RE: [gmx-users] liquid/liquid

Easiest way is probably set up the appropriate sized box for molecule 2, randomly distributed molecule 3 in appropriate number through it (genbox), then solvate that box with molecule 2, then combine that box with solvated box containing molecule 1. Catch ya, Dr. Dallas Warren Medicinal

Re: [gmx-users] sphere around a protein

Hello, Thanks Justin, I am getting somewhere but still running into problems. Okay, I have a 6 nm sphere (one Li ion surrounded by 1:1 water-methanol mixture) in 12 nm box. I did the following: editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro genbox -cp onlyli.gro -cs mix.gro

Re: [gmx-users] sphere around a protein

shivangi nangia wrote: Hello, Thanks Justin, I am getting somewhere but still running into problems. Okay, I have a 6 nm sphere (one Li ion surrounded by 1:1 water-methanol mixture) in 12 nm box. I did the following: editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro genbox -cp

Re: [gmx-users] sphere around a protein

Dear Justin, No. I am still preparing the system. I want the protein in the solvent sphere. On Sun, May 8, 2011 at 9:29 PM, Justin A. Lemkul jalem...@vt.edu wrote: shivangi nangia wrote: Hello, Thanks Justin, I am getting somewhere but still running into problems. Okay, I have a

Re: [gmx-users] sphere around a protein

shivangi nangia wrote: Dear Justin, No. I am still preparing the system. I want the protein in the solvent sphere. I see now. You're setting a 12-nm cubic box, but then using a shell of 6 nm, which causes neighbor searching to occur throughout the entire box. The maximum value of

Re: [gmx-users] ambar to opls force field

Hello Justin, Here I have done some analysis. The original value reported in J.Chem. Phys. 124, 024503 2006, paper are Kbond = 443153.3808 kJ/mol nm**2 Kangle = 317.5656 kJ/mol rad**2. Below are the results for the dielectric constant of water.I made the .itp file pasted below the table. Bond

Re: [gmx-users] ambar to opls force field

Nilesh Dhumal wrote: Hello Justin, Here I have done some analysis. The original value reported in J.Chem. Phys. 124, 024503 2006, paper are Kbond = 443153.3808 kJ/mol nm**2 Kangle = 317.5656 kJ/mol rad**2. Below are the results for the dielectric constant of water.I made the .itp file

Re: [gmx-users] How to recenter solvent around solute

Hi, On Sat, May 7, 2011 at 9:45 PM, Justin A. Lemkul jalem...@vt.edu wrote: Please clarify - do you wish to maintain the original triclinic representation (as -ur tric does) or do you wish to see the octahedral representation (as -pbc mol -ur compact gives)? My answer was based on your

Re: [gmx-users] sphere around a protein

Hi Justin, I used 15 nm cubic box and 6 nm shell. I again tried to insert only 1 histidine molecule in the sphere. I get the same error Fatal error: 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 the cut-off. On

Re: [gmx-users] How to recenter solvent around solute

On 9/05/2011 2:01 PM, Dimitar Pachov wrote: Hi, On Sat, May 7, 2011 at 9:45 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Please clarify - do you wish to maintain the original triclinic representation (as -ur tric does) or do you wish to see the octahedral

[gmx-users] Re: gmx-users Digest, Vol 85, Issue 61

: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110508/3d2858ce/attachment-0001.html -- Message: 2 Date: Sun, 08 May 2011 17:12:33 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] sphere around a protein To: Discussion list

[gmx-users] regarding creating tabulated potentials

dear gmx users, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or

Re: [gmx-users] Re: gmx-users Digest, Vol 85, Issue 61

On 9/05/2011 3:40 PM, Maria Hamilton wrote: Hi Dallas Please do not respond to whole digests - it confuses the archive. Cut out the relevant part and reply to it. Also, please choose a meaningful subject line. You said that Easiest way is probably set up the appropriate sized box for

[gmx-users] regarding nacl simulation in water using tabulated potentials

dear gmx users, i have to simulate nacl in water...the system is acubic box with just one na adn one cl ion in tip3p water.i wanted to use a buckingham potential for na adn cl interaction and lennard jones for water -ion intercation.i really dont have any idea on how to do

Re: [gmx-users] RE: gmx-users Digest, Vol 85, Issue 53

On 9/05/2011 9:10 AM, Ryan S Davis (rsdavis1) wrote: I am not sure if I replied to this thread correctly, but anyway. Please use a relevant subject line. I tried the things you guys suggested, but I still cant get it to work. You were right $HOME does have a slash in front but I am not

Re: [gmx-users] regarding nacl simulation in water using tabulated potentials

On 9/05/2011 3:46 PM, sreelakshmi ramesh wrote: dear gmx users, i have to simulate nacl in water...the system is acubic box with just one na adn one cl ion in tip3p water.i wanted to use a buckingham potential for na adn cl interaction and lennard jones for water