Re: [gmx-users] how to make topol.top file for mixed solution

cuong nguyen wrote: Dear, Thanks a lot Justin. I created a box containing mixed solution of 20 hexanol molecues and 20 octanol molecules in water. However, when I run grompp and mdrun commands, gromacs noticed errors with the topol.top file for this mixed system. So please help me to

Re: [gmx-users] refcoord_scaling

On 7/11/2011 4:53 PM, khuchtumur bumerdene wrote: Hi, I have a question about refcoord_scaling option and its role in pressure coupling. What I'm currently doing is just running the lysozyme tutorial on my own protein. I've so far had successful runs when equilibrating on my own machine,

[gmx-users] orca and qm/mm

Dear all users: According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and  BASENAME.ORCAINFO as told in the instruction. BASENAME=pyp_qm here is the BASENAME.ORCAINFO file: ! RKS

[gmx-users] orca and qm/mm

All users:   According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and  BASENAME.ORCAINFO as told in the instruction. BASENAME=pyp_qm here is the BASENAME.ORCAINFO file: ! RKS B3LYP/G

Re: [gmx-users] orca and qm/mm

Try not leaving QMmethod andQMbasis entries empty even if these data are read from orca input (in BASENAME.ORCAINFO). You can check in the input files (.inp) generated by GROMACS the actual commands used by ORCA. El 07/11/11 13:54, xi zhao escribió: All users: According to

[gmx-users] umbrella sampling with pull=constraint

Hello, I have done umbrella sampling with pull=umbrella and I found that the pulling group has high fluctuations and sometimes moving out of the periodic box. I think that the harmonic potential is not properly applied and thus the pulling group is not retained with the specified COM distance

Re: [gmx-users] orca and qm/mm

Just put something in QMMMscheme etc.. This will subsequently be overwritten by whatever you have in your ORCA file. Micha On 07/11/11 12:54, xi zhao wrote: All users: According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code http://wwwuser.gwdg.de/%7Eggroenh/qmmm.html#code, I want to

[gmx-users] Re 1. orca and qm/mm (xi zhao)

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[gmx-users] umbrella sampling with pull=constraint

Dear Vijay: Can you please provide evidence for your claim that the harmonic potential is not applied properly, since you may decide to use pull=umbrella once you have set that up correctly. Importantly, movement out of the unit-cell is not a problem, as discussed a lot on this list.

[gmx-users] PBC - Protein - ligand

Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow: 1. First make your molecules whole if you want them whole trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o

[gmx-users] Re:umbrella sampling with pull=constraint

If you use constraints it would not be umbrella sampling, where you need to sample around a restraint structure to get the histograms for WHAM or another analysis-technic. So if you want to do umbrella sampling either make to box bigger and/or make the restraints harder. But you can also use

Re: [gmx-users] PBC - Protein - ligand

Hi Steven, Don't use -ur compact in the first step and see if that solves the problem. Oh, and be sure that the thing is not just diffusing. There was a thread lately where a diffusing ligand drove someone mad trying to remove the 'jumps'. Cheers, Tsjerk On Mon, Nov 7, 2011 at 3:08 PM, Steven

Re: [gmx-users] PBC - Protein - ligand

Steven Neumann wrote: Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow: 1. First make your molecules whole if you want them whole trjconv -f md.trr -s

回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)

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回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)

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Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)

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[gmx-users] Re: umbrella sampling with pull=constraint

Hello, Thanks for the suggestions. I did umbrella simulation for 20ns and the pull force is as below. 19960.-6.78192 19962.33.3579 19964.-3.1808 19966.-15.0304 19968.-55.4436 19970.-38.9422 19972.-9.41927 19974.-5.95981 19976.

[gmx-users] Re: umbrella sampling with pull=constraint

and also I tried to plot the PMF curve from this data, I got few warning messages like no data point in bin 20, You may not get a reasonable profile. Check your histograms!. the histogram shows poor sampling from 0.6 nm to 0.7 nm, and the windows in this position completely overlaps at 0.5-0.6 nm.

Re: [gmx-users] Re: umbrella sampling with pull=constraint

Vijayaraj wrote: and also I tried to plot the PMF curve from this data, I got few warning messages like no data point in bin 20, You may not get a reasonable profile. Check your histograms!. the histogram shows poor sampling from 0.6 nm to 0.7 nm, and the windows in this position completely

[gmx-users] lipid bilayer and umbrella sampling

Dear Gromacs Users,     I am trying to extract the potential of mean force of a small molecule in a DPPC bilayer. To this end, I applied the methodology described in an online manual written by Justin Lemkul. My problem is when I run biasing simulations of the molecule near the interface

Re: [gmx-users] PBC - Protein - ligand

On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow: 1. First

[gmx-users] Re: umbrella sampling with pull=constraint

My system is a self-assembled cyclic peptide, I am trying to extract PMF to pull one of the terminal cyclic peptide. I have collected 25 windows starting from 0.5nm with 0.05nm window size. the histogram shows up to 0.7nm all the windows are overlapped around 0.5nm, and poor sampling from 0.6 to

[gmx-users] request for comments on profile.xvg (PMF) courve

Dear gmx users, my goal is to aquire a PMF courve of two amino-acids (ASP and LYS) of which one is pulled from the other. I followed Justin's tutorial on umbrella sampling. Here are the results. profile.xvg: http://przemekbartha.pl/upload/profile.png histo.xvg:

Re: [gmx-users] lipid bilayer and umbrella sampling

Giovanni Mancini wrote: Dear Gromacs Users, I am trying to extract the potential of mean force of a small molecule in a DPPC bilayer. To this end, I applied the methodology described in an online manual written by Justin Lemkul. My problem is when I run biasing simulations of the

Re: [gmx-users] Re: umbrella sampling with pull=constraint

Vijayaraj wrote: My system is a self-assembled cyclic peptide, I am trying to extract PMF to pull one of the terminal cyclic peptide. I have collected 25 windows starting from 0.5nm with 0.05nm window size. the histogram shows up to 0.7nm all the windows are overlapped around 0.5nm, and poor

Re: [gmx-users] request for comments on profile.xvg (PMF) courve

Przemek Bartha wrote: Dear gmx users, my goal is to aquire a PMF courve of two amino-acids (ASP and LYS) of which one is pulled from the other. I followed Justin's tutorial on umbrella sampling. Here are the results. profile.xvg: http://przemekbartha.pl/upload/profile.png histo.xvg:

[gmx-users] problem while running production md

dear gmx-users, i am getting the following error message while running production md (mpirun).. Step 102, time 0.204 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 122.760095, max 2890.435059 (between atoms 5092 and 5090) bonds that rotated more than 30 degrees: atom 1

Re: [gmx-users] problem while running production md

ansu...@physics.iisc.ernet.in wrote: dear gmx-users, i am getting the following error message while running production md (mpirun).. Step 102, time 0.204 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 122.760095, max 2890.435059 (between atoms 5092 and 5090) bonds

[gmx-users] lipid bilayer and umbrella sampling

If you add position restraints to your DPPC molecules, then you are changing your effective order parameter. The PMF for the solute along the normal to a restrained bilayer will have a different shape than a PMF for the solute along the normal to an urestrained bilayer. Whether or not this is

Re: [gmx-users] PBC - Protein - ligand

Hi Steven, Step 2: Cluster your molecules. This is where you have to forge a reference frame that you can use to remove jumps from your trajectory. If the ligand is not with the protein at the start, you'll have to shift it so that it is. Maybe -pbc cluster is your friend there. I do assume that

[gmx-users] Re: PBC - Protein - ligand

Hi Tsjerk, Thank you. Unfortunately my ligand is not with protein. I put my ligand around my protein (in water) running separate simulations to see where can it bind. It is close to protein but not within. Any other suggestion? I used also pbc -res so I observe my ligand close to protein but

[gmx-users] gromacs query for force field in vaccum and liquid

I want to simulate membrane protein in vaccum so let me know which force field i can use for it. Also I m doing simulation for the same protein in liquid using OPLS force field.Please tell me is it correct? -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Re: problem while running production md

dear gmx-users, i am getting the following error message while running production md (mpirun).. Step 102, time 0.204 (ps)  LINCS WARNING relative constraint deviation after LINCS: rms 122.760095, max 2890.435059 (between atoms 5092 and 5090) bonds that rotated more than 30 degrees:  

Re: [gmx-users] Re: PBC - Protein - ligand

Steven Neumann wrote: Hi Tsjerk, Thank you. Unfortunately my ligand is not with protein. I put my ligand around my protein (in water) running separate simulations to see where can it bind. It is close to protein but not within. Any other suggestion? I used also pbc -res so I observe my

[gmx-users] Water Liquid-vapor interface: Negative surface tension by virial formula?

Dear GMXers, I'm computing the liquid-vapor surface tension for SPC/E water using GROMACS 4.5.3. The initial water box dimension is 3nm*3nm*3nm, containing 1807 water molecules, which is extended in z direction to a length of 12nm, to create two liquid-vapor interfaces. The ensemble is NVT. The

Re: [gmx-users] PBC - Protein - ligand

On 8/11/2011 3:17 AM, Steven Neumann wrote: On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the

Re: [gmx-users] gromacs query for force field in vaccum and liquid

On 8/11/2011 8:24 AM, Anushree Tripathi wrote: I want to simulate membrane protein in vaccum so let me know which force field i can use for it. Probably none of them - they were all parametrized on condensed-phase data. In order to do such a simulation, you are going to have to establish a

[gmx-users] g_hbond -hbn

Hi Gmxers, I used g_hbond -n protein.ndx -hbn output.xvg to get the index of all the atoms forming H-bond with the protein, but since H-Bonds should be dynamic as time evolves, I should see changing number of HBonds in the output.xvg which I have not seen yet. Kinda confused. Thanks, Yao 

Re: [gmx-users] g_hbond -hbn

Yao Yao wrote: Hi Gmxers, I used g_hbond -n protein.ndx -hbn output.xvg to get the index of all the atoms forming H-bond with the protein, but since H-Bonds should be dynamic as time evolves, I should see changing number of HBonds in the output.xvg which I have not seen yet. Kinda confused.

Re: [gmx-users] B-factor to large? Input for TLS

On 5/11/2011 11:05 AM, Henri Mone wrote: Dear Gromacs Users and Experts, I want to calculate from my xtc trajectory the B-factor and the anisotropic temperature factor. I'm using following gromacs command: $ g_rmsf -f traj.xtc -o rmsf.xvg -oq bfac.pdb -ox bfac2.pdb -s structure.pdb Does

[gmx-users] Problems with deuterium graphs

Dear All, I run a MD simulation on a membrane protein using DPPC and I performed a deuterium order parameters on the trajectory. As I'm a newbie, could you kindly help me to give an interpretation of these graphs? You can open them at: sn1 http://www.freeimagehosting.net/137c9 sn2

[gmx-users] Sorry for posting twice

I'm sorry for having post the message about deuterium twice. It ws a mistake -- 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

[gmx-users] A question about deuteriu order parameters graph

Dear All, I run a MD simulation on a membrane protein using DPPC and I performed a deuterium order parameters on the trajectory. As I'm a newbie, could you kindly help me to give an interpretation of these graphs? You can open them at: sn1 http://www.freeimagehosting.net/137c9 sn2

Re: [gmx-users] how to make topol.top file for mixed solution

Dear, I created a 5 5 2 box containing 15 mibc and 15 decanol molecues by using two comands: *genbox -ci decanol.gro -nmol 15 -box 5 5 2 -o layer.gro -p decanol.top genbox -cp layer.gro -ci decanol.gro -nmol 15 -box 5 5 2 -o box.gro -p mibc.top* then I filled this mixture by water to create other

[gmx-users] remd with different potential at different temperature

dear teacher, how can i do remd with different non-bond potential at different temperature ? easy to say ,can i use different *.top at diferent temperature. if not ,can you give me some suggestions to rewrite the gromacs codes. thanks!! regards, PHD, Bo Du Department of Polymer Science and

Re: [gmx-users] how to make topol.top file for mixed solution

On 8/11/2011 5:36 PM, cuong nguyen wrote: Dear, I created a 5 5 2 box containing 15 mibc and 15 decanol molecues by using two comands: /genbox -ci decanol.gro -nmol 15 -box 5 5 2 -o layer.gro -p decanol.top genbox -cp layer.gro -ci decanol.gro -nmol 15 -box 5 5 2 -o box.gro -p mibc.top/

Re: [gmx-users] remd with different potential at different temperature

On 8/11/2011 5:43 PM, ?? wrote: dear teacher, how can i do remd with different non-bond potential at different temperature ? easy to say ,can i use different *.top at diferent temperature. Probably. Try a simple case and see. The REMD implementation checks only certain critical quantities

Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)

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