Re: [gmx-users] KALP15 in DPPC

On 2/1/18 6:14 PM, negar habibzadeh wrote: hi . I want to measure the distance between center of membrane and a peptide . how can i use gmx distance ?? What have you tried? Did it work or cause problems? -Justin On Wed, Jan 31, 2018 at 8:13 PM, Justin Lemkul wrote:

Re: [gmx-users] KALP15 in DPPC

hi . I want to measure the distance between center of membrane and a peptide . how can i use gmx distance ?? On Wed, Jan 31, 2018 at 8:13 PM, Justin Lemkul wrote: > > > On 1/30/18 7:00 PM, negar habibzadeh wrote: > >> hi. in my dopc.gro file i have 128 dopc ,5120 water (sol)

Re: [gmx-users] KALP15 in DPPC

On 1/30/18 7:00 PM, negar habibzadeh wrote: hi. in my dopc.gro file i have 128 dopc ,5120 water (sol) with box size of 6.5 6.5 7.5 .i increase z direction from 7.5 nm to 10 nm ,how can i add some extra water more than 5120 ?? Just run gmx solvate again. -Justin On Mon, Jan 29, 2018

Re: [gmx-users] KALP15 in DPPC

hi. in my dopc.gro file i have 128 dopc ,5120 water (sol) with box size of 6.5 6.5 7.5 .i increase z direction from 7.5 nm to 10 nm ,how can i add some extra water more than 5120 ?? On Mon, Jan 29, 2018 at 5:41 PM, Justin Lemkul wrote: > > > On 1/28/18 3:22 PM, negar

Re: [gmx-users] KALP15 in DPPC

On 1/28/18 3:22 PM, negar habibzadeh wrote: my peptide is a cpp (cell penetrating peptide) . i am going to simulation this peptide in dopc bilayer , i did lots of methods to build the system but in nvt step i saw water inside dopc (i used posre for water but when i removed it to run npt or md

Re: [gmx-users] KALP15 in DPPC

my peptide is a cpp (cell penetrating peptide) . i am going to simulation this peptide in dopc bilayer , i did lots of methods to build the system but in nvt step i saw water inside dopc (i used posre for water but when i removed it to run npt or md ,my problem was not solved ).Is it true that my

Re: [gmx-users] KALP15 in DPPC

On 1/25/18 12:17 PM, negar habibzadeh wrote: How much time is needed to run ? i changed from 100 ps ( restrained equilibration run ( nvt)) to 1 ns(1000ps) . but when i did npt (without water and lipids restraints) again i saw water inside membrane. I don't know. Such protocols are usually

Re: [gmx-users] KALP15 in DPPC

How much time is needed to run ? i changed from 100 ps ( restrained equilibration run ( nvt)) to 1 ns(1000ps) . but when i did npt (without water and lipids restraints) again i saw water inside membrane. On Wed, Jan 24, 2018 at 10:51 PM, Justin Lemkul wrote: > > > On 1/24/18

Re: [gmx-users] KALP15 in DPPC

On 1/24/18 11:16 AM, negar habibzadeh wrote: i did it but when i removed the restraints from water to equilibrate again ,(after new equilibration ) i saw some water molecules inside the membrane again. what can i do ? Let the restrained equilibration run longer. Make sure you're not

Re: [gmx-users] KALP15 in DPPC

i did it but when i removed the restraints from water to equilibrate again ,(after new equilibration ) i saw some water molecules inside the membrane again. what can i do ? On Wed, Jan 24, 2018 at 4:24 PM, Justin Lemkul wrote: > > > On 1/24/18 5:02 AM, negar habibzadeh

Re: [gmx-users] KALP15 in DPPC

On 1/24/18 5:02 AM, negar habibzadeh wrote: hi . i am doing simulation of peptide in DOPC bilayer. i have dopc.itp , dopc.pdb, dopc.gro , peptide.itp , sample.top for dopc , peptide.pdb,topol.top. i used below commands. gmx editconf -f peptide.gro -o pep.gro -box 6.35172 6.80701 7.49241

Re: [gmx-users] KALP15 in DPPC

hi . i am doing simulation of peptide in DOPC bilayer. i have dopc.itp , dopc.pdb, dopc.gro , peptide.itp , sample.top for dopc , peptide.pdb,topol.top. i used below commands. gmx editconf -f peptide.gro -o pep.gro -box 6.35172 6.80701 7.49241 -c (it corresponds to the x/y/z box vectors of

Re: [gmx-users] KALP15 in DPPC

On 1/21/18 1:23 PM, negar habibzadeh wrote: hi . in vmd how can i find special number for each atom? i want to delete those atoms from my gro file. You can label atoms by clicking on them in label mode. If you have further questions about VMD, post to their mailing list. -Justin tnx

Re: [gmx-users] KALP15 in DPPC

hi . in vmd how can i find special number for each atom? i want to delete those atoms from my gro file. tnx On Mon, Jan 15, 2018 at 9:12 PM, Justin Lemkul wrote: > > > On 1/15/18 10:56 AM, negar habibzadeh wrote: > >> tnx so much >> i got nvt.tpr and now i want to run it but

Re: [gmx-users] KALP15 in DPPC

On 1/15/18 10:56 AM, negar habibzadeh wrote: tnx so much i got nvt.tpr and now i want to run it but i am getting this error : Fatal error: Too many LINCS warnings (5258) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable

Re: [gmx-users] KALP15 in DPPC

tnx so much i got nvt.tpr and now i want to run it but i am getting this error : Fatal error: Too many LINCS warnings (5258) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is

Re: [gmx-users] KALP15 in DPPC

On 1/15/18 6:18 AM, negar habibzadeh wrote: tnx Justin . now I am doing Simulation of *5 *Peptide in DOPC Lipids I am following your tutorial, in NVT equilibration step I created index file , with program make_ndx (gmx make_ndx -f em.gro -o index.ndx) : 0 System : 30700 atoms

Re: [gmx-users] KALP15 in DPPC

tnx Justin . now I am doing Simulation of *5 *Peptide in DOPC Lipids I am following your tutorial, in NVT equilibration step I created index file , with program make_ndx (gmx make_ndx -f em.gro -o index.ndx) : 0 System : 30700 atoms 1 Other : 18744 atoms 2 FR1

Re: [gmx-users] KALP15 in DPPC

On 1/7/18 3:07 AM, negar habibzadeh wrote: I am doing Simulation of *γ-AA*Peptide in DOPC Lipids I am following your tutorial When I use inflategro script For my System I have got Output System_inflated.gro file with certain message in Command prompt as follows . The Below Message Shows

[gmx-users] KALP15 in DPPC

I am doing Simulation of *γ-AA*Peptide in DOPC Lipids I am following your tutorial When I use inflategro script For my System I have got Output System_inflated.gro file with certain message in Command prompt as follows . The Below Message Shows That There is No Lipid Molecules Are Deleted

Re: [gmx-users] KALP15 in DPPC: Bilayer out of solvation box

On 1/1/18 10:01 PM, Seketoulie Keretsu wrote: Dear Experts I am currently doing the gromacs tutorial for simulation of membrane protein (KALP15 in DPPC by Justin A. Lemkul). I came across several challenges most of which I could resolve. However, the result after solvation wasn't as expected.

Re: [gmx-users] KALP15 in DPPC: Bilayer out of solvation box

Hi, On Tue, Jan 2, 2018 at 3:02 AM Seketoulie Keretsu wrote: > Dear Experts > > I am currently doing the gromacs tutorial for simulation of membrane > protein (KALP15 in DPPC by Justin A. Lemkul). I came across several > challenges most of which I could resolve. However,

[gmx-users] KALP15 in DPPC: Bilayer out of solvation box

Dear Experts I am currently doing the gromacs tutorial for simulation of membrane protein (KALP15 in DPPC by Justin A. Lemkul). I came across several challenges most of which I could resolve. However, the result after solvation wasn't as expected. That is, a small portion of the DPPC bilayer was

Re: [gmx-users] KALP15 in DPPC Analysis section

On 10/27/16 2:18 PM, Sailesh Bataju wrote: Hi, I've been following KAlP15 in DPPC tutorial successfully but now I stuck in the last Analysis section. I googled the problem there's nothing out. The question is so simple it's just a misunderstanding. In the 2nd part Density of the Membrane the

[gmx-users] KALP15 in DPPC Analysis section

Hi, I've been following KAlP15 in DPPC tutorial successfully but now I stuck in the last Analysis section. I googled the problem there's nothing out. The question is so simple it's just a misunderstanding. In the 2nd part Density of the Membrane the code is # gmx make_ndx -f md_0_1.tpr -o

[gmx-users] KALP15 in DPPC: NPT: File input/output error: nvt.gro

Dear gmx-users, Ok I figured out the lipid packing from my previous questionhttps://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096396.html  But now when I am at this NPT

[gmx-users] KALP15 in DPPC: lipid packing: deleting and shrinking lipids: why are the number of lipids not decreasing?

Dear gmx-users, I am not confident doing the lipid packing in this tutorial (using Maximin 3 instead of KALP15): http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html And my biggest problem is this error (see my hypothesized solution at the end

[gmx-users] KALP15 in DPPC tutorial: system_shrink1.gro error?

Dear gmx-users: Following this tutorial, using Maximin 3 instead of KALP15 and charmm36 instead of gromos53a6: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html When I do this: /usr/local/gromacs/bin/gmx grompp -f minim.mdp -c