Re: [gmx-users] Umbrella Sampling tutorial

On 11/10/13 9:14 AM, shahab shariati wrote: Dear Justin Very thanks for your reply. What you described earlier should not be attempted with "distance" geometry. It won't work very well. The use of restraints is almost NEVER necessary, especially in the case where the reference group > is mu

Re: [gmx-users] Umbrella Sampling tutorial

On 11/10/13 5:31 AM, shahab shariati wrote: Dear Justin Thanks for your reply. You are right. I should not extrapolate too literally from your tutorial to my system. But, I have a general question: There is 2 groups in COM pulling method (reference group + pull group). If I want to use pu

Re: [gmx-users] Umbrella Sampling tutorial

On 11/9/13 9:38 AM, shahab shariati wrote: Dear Justin Thanks for your explanation. My system contains lipid bilayer + drug + water molecules. I want to calculate Potential of mean force as a function of the distance between the centers of mass of drug and the lipid bilayer. Box vector alon

Re: [gmx-users] Umbrella Sampling tutorial

On 11/9/13 8:22 AM, shahab shariati wrote: Daer Justin I studied your tutorial (Umbrella Sampling). It is very beneficial for me. The system you considered was the dissociation of a single peptide from the growing end of an protofibril. You considered following parameters: Chain_B: referenc

Re: [gmx-users] umbrella sampling using pull codes

n list for GROMACS users Subject: Re: [gmx-users] umbrella sampling using pull codes On 9/12/13 10:18 PM, mjyang wrote: Dear Justin, Thanks for your reply. I checked the content in pullx.xvg file as follows: # GRowing Old MAkes el Chrono Sweat #

RE: [gmx-users] umbrella sampling using pull codes

s.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul [jalem...@vt.edu] Sent: Friday, September 13, 2013 10:33 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] umbrella sampling using pull codes On 9/12/13 10:18 PM, mjyang wrote: > Dear Justin, > > Thanks for yo

Re: [gmx-users] umbrella sampling using pull codes

On 9/12/13 10:18 PM, mjyang wrote: Dear Justin, Thanks for your reply. I checked the content in pullx.xvg file as follows: # GRowing Old MAkes el Chrono Sweat # @title "Pull COM" @xaxis label "Time (ps)" @yaxis label "Posit

RE: [gmx-users] umbrella sampling using pull codes

.org] On Behalf Of Justin Lemkul [jalem...@vt.edu] Sent: Thursday, September 12, 2013 10:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] umbrella sampling using pull codes On 9/12/13 9:55 AM, mjyang wrote: > Dear GMX users, > > I'd like to perform the um

Re: [gmx-users] umbrella sampling using pull codes

On 9/12/13 9:55 AM, mjyang wrote: Dear GMX users, I'd like to perform the umbrella sampling using the pull codes in gromacs. The reaction coordinate is defined as the distance between the center of mass (DCOM) of two domains in a protein. The following script is used: ---

Re: [gmx-users] Umbrella sampling simulations using make_edi with -restrain and -harmonic

Hi Po-chia, On Sep 10, 2013, at 9:53 AM, "Chen, Po-chia" wrote: > Hi all, > I can't seem to find the correct combination of EDI parameters impose a > harmonically-constrained simulation along an eigenvector in GROMACS 4.6.2, > and I'd like to confirm that the inputs I have are actually correct

Re: [gmx-users] Umbrella Sampling PMF

On 9/1/13 1:39 AM, Shima Arasteh wrote: Hi, I ran US on an ion through a channel inserted in a bilayer. I used g_wham and got the profile output. In the visualized profile, I see a region that the plot shows a flat line and it seems the data is missed there. Would you please let me know wh

Re: [gmx-users] Umbrella sampling - position restraints

On 8/8/13 3:57 PM, rookie417 wrote: Dear GROMACS users, I followed the Umbrella Sampling tutorial to run a simple simulation of pulling polymer chain from the surface of micelle. I used position restraints for the initial equilibration, however I realized a typo in the define=-DPOSRES mdp file

Aw: Re: [gmx-users] Umbrella Sampling

endet: Mittwoch, 31. Juli 2013 um 12:46 Uhr Von: "Steven Neumann" An: "Discussion list for GROMACS users" Betreff: Re: [gmx-users] Umbrella Sampling They do not dissociate...Are you sure? My mdp specifies only ligand as a pull_group1. I think it would change having ions in this grou

Re: [gmx-users] Umbrella Sampling

I am do not want to choose different pulling conditions as I build a model for specific force constant and pulling rate in given force filed. I think restraining would help much more to then exclude the ions impact. Steven On Wed, Jul 31, 2013 at 12:49 PM, Steven Neumann wrote: > Thank you a lo

Re: [gmx-users] Umbrella Sampling

Thank you a lot! On Wed, Jul 31, 2013 at 12:46 PM, Justin Lemkul wrote: > > > On 7/31/13 6:52 AM, Steven Neumann wrote: > >> But even though on the other hand that could be more realistic free energy >> which could be compare to experiment which also involves ions. Would >> Justin >> please com

Re: [gmx-users] Umbrella Sampling

On 7/31/13 6:52 AM, Steven Neumann wrote: But even though on the other hand that could be more realistic free energy which could be compare to experiment which also involves ions. Would Justin please comment on this? I can offer you nothing more than a hand-waving explanation of what I think

Re: [gmx-users] umbrella Sampling and PMF- Error estimation

Thank you for your reply Dr. Justin On 7/31/13, Justin Lemkul wrote: > > > On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote: >> Hi everyone >> >> How can we have an error estimation for Gibbs binding free energy when >> I do umbrella sampling and PMF profile? >> >> Actually I did an umbrella sampling

Re: [gmx-users] umbrella Sampling and PMF- Error estimation

On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote: Hi everyone How can we have an error estimation for Gibbs binding free energy when I do umbrella sampling and PMF profile? Actually I did an umbrella sampling for protein and ligand complex and I have a PMF profile now but I do not know how much i

Re: [gmx-users] Umbrella Sampling

But even though on the other hand that could be more realistic free energy which could be compare to experiment which also involves ions. Would Justin please comment on this? On Wed, Jul 31, 2013 at 11:46 AM, Steven Neumann wrote: > They do not dissociate...Are you sure? My mdp specifies only li

Re: [gmx-users] Umbrella Sampling

They do not dissociate...Are you sure? My mdp specifies only ligand as a pull_group1. I think it would change having ions in this group included. On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs wrote: > > >will get the PMF profile for my > >ligand binding or ligand and two ions binding? > > It wo

Re: [gmx-users] Umbrella Sampling _ pulled ion

= com Would you please let me know your suggestions ? Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh Cc: Sent: Wednesday, July 24, 2013 9:41 PM Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion On 7/24/13 11:53 AM, Shima Arasteh wrote: Yes

Re: [gmx-users] Umbrella Sampling _ pulled ion

know your suggestions ?   Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh Cc: Sent: Wednesday, July 24, 2013 9:41 PM Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion On 7/24/13 11:53 AM, Shima Arasteh wrote: > Yes, Thanks. > > Would you

Re: [gmx-users] Umbrella Sampling _ pulled ion

odd result for npt_US or md_US? Many many thanks for your time and suggestions.   Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Wednesday, July 24, 2013 8:05 PM Subject: Re: [gmx-users] Umbrella Sampling _ pulle

Re: [gmx-users] Umbrella Sampling _ pulled ion

On 7/24/13 11:30 AM, Shima Arasteh wrote: Hi, I am trying to run US on a system composed of lipid bilayer/ ion/ water/ peptide. The peptide is inserted through the lipid bilayer and I' d like to study the ion conduction through the peptide across the membrane. In order to do so, I tried to

Re: [gmx-users] Umbrella Sampling settings

[gmx-users] Umbrella Sampling settings On 7/12/13 11:32 AM, Shima Arasteh wrote: > > > > Allright. > As I said earlier, my system is a lipid bilayer. A channel is inserted in it > and I want to run US on this system. > An ion is considered in center of the each window, the rea

Re: [gmx-users] Umbrella Sampling settings

On 7/12/13 11:32 AM, Shima Arasteh wrote: Allright. As I said earlier, my system is a lipid bilayer. A channel is inserted in it and I want to run US on this system. An ion is considered in center of the each window, the reaction coordinate is set to z, so the group which is pulled is an

Re: [gmx-users] Umbrella Sampling settings

group? Would you please give me any suggestions? Thanks for all your time and consideration. Sincerely, Shima - Original Message - From: Justin Lemkul To: Discussion list for GROMACS users Cc: Sent: Friday, July 12, 2013 1:41 AM Subject: Re: [gmx-users] Umbrella Sampling settings On

Re: [gmx-users] Umbrella Sampling settings

group? Would you please give me any suggestions? Thanks for all your time and consideration. Sincerely, Shima - Original Message - From: Justin Lemkul To: Discussion list for GROMACS users Cc: Sent: Friday, July 12, 2013 1:41 AM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/

Re: [gmx-users] Umbrella Sampling settings

ima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Friday, July 12, 2013 1:37 AM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/11/13 4:21 PM, Shima Arasteh wrote: Hi, I want to run Umbrella Sampling on m

Re: [gmx-users] Umbrella Sampling settings

013 1:37 AM Subject: Re: [gmx-users] Umbrella Sampling settings On 7/11/13 4:21 PM, Shima Arasteh wrote: > Hi, > > I want to run Umbrella Sampling on my system. In initial configurations, an > ion is located in center of the window. > Some mdp file settings for running US, as I

Re: [gmx-users] Umbrella Sampling settings

On 7/11/13 4:21 PM, Shima Arasteh wrote: Hi, I want to run Umbrella Sampling on my system. In initial configurations, an ion is located in center of the window. Some mdp file settings for running US, as I found in US tutorial are : ; Pull code pull= umbrella pull_geometry = dist

Re: [gmx-users] Umbrella sampling- force vs time plots

On 7/9/13 12:56 PM, rookie417 wrote: Hello all, I am trying to understand the force vs time plots using Gromacs' umbrella sampling method. I am trying to pull a short polymer chain from the interior of a micelle and see what the PMF looks like. I use the following parameters to run the pulling

Re: [gmx-users] umbrella sampling on GPU with Gromacs 4.6

Great, thanks! I'll give it a try. On 7/8/13 1:02 PM, Justin Lemkul wrote: On 7/8/13 12:58 PM, Justin Lemkul wrote: On 7/8/13 12:56 PM, Diana Fusco wrote: Hi Justin, I have actually followed your tutorial to perform umbrella sampling on CPU and it worked great. Can I use the same file fo

Re: [gmx-users] umbrella sampling on GPU with Gromacs 4.6

On 7/8/13 12:58 PM, Justin Lemkul wrote: On 7/8/13 12:56 PM, Diana Fusco wrote: Hi Justin, I have actually followed your tutorial to perform umbrella sampling on CPU and it worked great. Can I use the same file for GPU acceleration or I have to add some fields and commands? There's nothi

Re: [gmx-users] umbrella sampling on GPU with Gromacs 4.6

On 7/8/13 12:56 PM, Diana Fusco wrote: Hi Justin, I have actually followed your tutorial to perform umbrella sampling on CPU and it worked great. Can I use the same file for GPU acceleration or I have to add some fields and commands? There's nothing GPU-specific in the .mdp file. -Justin

Re: [gmx-users] umbrella sampling on GPU with Gromacs 4.6

Hi Justin, I have actually followed your tutorial to perform umbrella sampling on CPU and it worked great. Can I use the same file for GPU acceleration or I have to add some fields and commands? Thanks! Diana On 7/8/13 12:47 PM, Justin Lemkul wrote: On 7/8/13 12:08 PM, Diana Fusco wrote:

Re: [gmx-users] umbrella sampling on GPU with Gromacs 4.6

On 7/8/13 12:08 PM, Diana Fusco wrote: Hello, I'd like to know if it is possible with Gromacs 4.6 to perform umbrella sampling using GPU with orientational restraints. If it is, can you give me a simple example of mdp file to see how it works? As to whether or not it works, mdrun will compl

Re: [gmx-users] UMBRELLA SAMPLING

It's just the xvv file. g_wham uses the letter 'z' to denote the reaction coordinate. Erik On 2 Jul 2013, at 11:32, battis...@libero.it wrote: > > > > > > > Dear users and experts > > I'm doing an umbrella-samplig calculation to obtain the PMF when two > structure (A and B) are at vario

Re: [gmx-users] Umbrella Sampling Force component output

Thanks Erik On 06/12/2013 01:50 PM, Erik Marklund wrote: Hi, No, I'm afraid not. pull-dim not only determines what components are to be printed, it also determines in what dimensions the force is to be applied during the simulation. Erik On 12 Jun 2013, at 13:32, Kenny Bravo Rodriguez wro

Re: [gmx-users] Umbrella Sampling Force component output

Hi, No, I'm afraid not. pull-dim not only determines what components are to be printed, it also determines in what dimensions the force is to be applied during the simulation. Erik On 12 Jun 2013, at 13:32, Kenny Bravo Rodriguez wrote: > Dear Gromacs Users, > > I runned and Umbrella Sampli

Re: [gmx-users] umbrella sampling for two polymer interaction

Dear Lloyd, I have read that but my system is different regards, On Thu, May 30, 2013 at 8:28 PM, lloyd riggs wrote: > Dear Jiom, > > Look at justines tutorial, there's example pull .mdp. > > Stephan Watkins > > *Gesendet:* Donnerstag, 30. Mai 2013 um 14:44 Uhr > *Von:* "gromacs query" > *An

Re: [gmx-users] umbrella sampling tutorial

On 4/29/13 6:42 AM, Shima Arasteh wrote: Dear Justin, About Umbrella sampling tutorial, would you please let me know why you created an index file contains of chain A and chain B? Also, what's the meaning of 19 and 20 created by a text editoras groups.txt file? I can not understand this.

Re: [gmx-users] Umbrella sampling - regd

Dear Justin, Thank you very much for your quick reply. Regards, Ramesh. On Wed, Jan 2, 2013 at 10:24 AM, Justin Lemkul wrote: > > > On 1/1/13 11:48 PM, ramesh cheerla wrote: > >> Dear Gromacs users, >> >> I am performing umbrella samplin

Re: [gmx-users] Umbrella sampling - regd

On 1/1/13 11:48 PM, ramesh cheerla wrote: Dear Gromacs users, I am performing umbrella sampling simulations by selecting configurations with spacing window of 0.02nm from pulling simulations with the following options in .mdp file to get PMF along a axis

Re: [gmx-users] Umbrella sampling - chain A does not get pulled

On 12/12/12 5:26 PM, Justin Lemkul wrote: On 12/12/12 5:15 PM, Davide Mercadante wrote: Dear Justin, Thank you for your reply. To be sure I carefully ran the simulations again using the following .mdp file that includes the pull lines and -DPOSRES_B to restrain chain B from being pulled whe

Re: [gmx-users] Umbrella sampling - chain A does not get pulled

On 12/12/12 5:15 PM, Davide Mercadante wrote: Dear Justin, Thank you for your reply. To be sure I carefully ran the simulations again using the following .mdp file that includes the pull lines and -DPOSRES_B to restrain chain B from being pulled when chain A is being pulled (it is the .mdp fil

Re: [gmx-users] Umbrella sampling - chain A does not get pulled

Dear Justin, Thank you for your reply. To be sure I carefully ran the simulations again using the following .mdp file that includes the pull lines and -DPOSRES_B to restrain chain B from being pulled when chain A is being pulled (it is the .mdp file given in the tutorial): title = Umbrella

Re: [gmx-users] Umbrella sampling - chain A does not get pulled

On 12/11/12 2:40 AM, Davide Mercadante wrote: Dear Justin, I have been practicing umbrella sampling simulations following your tutorial step by step. I have just finished to perform the pull simulations to identify the configurations to use in the umbrella runs. I have used the distances.pl sc

Re: [gmx-users] Umbrella sampling - regd

Dear Justin, I am very thankful to you for your reply, you are correct, I have plotted the histo.xvg file in wrong manner. After plotting histograms in correct manner I have realized that my sampling is very poor as histograms and there overlapping is restricted to some regions only, no histogram

Re: [gmx-users] Umbrella sampling - regd

On 11/26/12 1:03 AM, ramesh cheerla wrote: Dear Gromacs users, I am calculating PMF for the ion permeation through a tunnel, using umbrella sampling. In my system I have some binding sites with ions, I have removed some ions from binding sites before pulling and In pulling simulations

Re: [gmx-users] Umbrella sampling after TMD of NAMD

It seems difficult to use RMSD as the reaction coordinate to do umbrella sampling simulations. Maybe you can try meta-dynamics in which you can use RMSD as a collective to get the free energy. It is implemented in a modified version of gromacs (GROMETA), or you can use PLUMED together with curr

Re: [gmx-users] Umbrella sampling after TMD of NAMD

On 10/17/12 9:17 AM, Netaly Khazanov wrote: Thanks. However, I can restrain the position of backbone (x,y,z -coordinates) while running umbrella sampling and treat it like reaction coordinate. Is it right? Maybe I am missing something. pull = umbrella pull_geometry = position ;pull_dim = Y

Re: [gmx-users] Umbrella sampling after TMD of NAMD

Thanks. However, I can restrain the position of backbone (x,y,z -coordinates) while running umbrella sampling and treat it like reaction coordinate. Is it right? Maybe I am missing something. pull = umbrella pull_geometry = position ;pull_dim = Y Y Y pull_start = yes pull_ngroups = 1 ;pull_grou

Re: [gmx-users] Umbrella sampling after TMD of NAMD

On 10/17/12 5:44 AM, Netaly Khazanov wrote: Of course I read Justin's tutorial. The reason I am asking is that I am not sure how to do it. As far as I am aware, there is no way to conduct umbrella sampling in this way using Gromacs. The PMF calculations that Gromacs does are based on restr

Re: [gmx-users] Umbrella sampling after TMD of NAMD

Of course I read Justin's tutorial. The reason I am asking is that I am not sure how to do it. On Wed, Oct 17, 2012 at 11:09 AM, Arman Mahboubi Soufiani < armansoufi...@gmail.com> wrote: > Hi, > > I recommend you Justin's tutorial on Umbrella Sampling > > http://www.bevanlab.biochem.vt.edu/Pages/

Re: [gmx-users] Umbrella sampling after TMD of NAMD

Hi, I recommend you Justin's tutorial on Umbrella Sampling http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html Regards Arman On Wed, Oct 17, 2012 at 10:47 AM, Netaly Khazanov wrote: > Dear All, > > I've performed TMD simulation using NAMDprogram. I'd lik

Re: [gmx-users] umbrella sampling (PMF) position discrepancy

Hello Gromacs users, The solution that ended up working is selecting a different pull_pbcatom0 from the reference group, the protein, such that the atom is approx. in the center of mass of the protein. I hope that others may find this useful, Thanks to Martin Vesper and Justin Lemkul for their i

Re: [gmx-users] Umbrella sampling-protein-ligand complex

On 9/28/12 2:19 PM, Archana Sonawani wrote: Dear Justin, So do I have to carry out umbrella sampling simulations separately for the three complexes or put the three ligands together with the protein and pull the ligands one by one to calculate the binding energy. I am confused. Each complex

Re: [gmx-users] Umbrella sampling-protein-ligand complex

Dear Justin, So do I have to carry out umbrella sampling simulations separately for the three complexes or put the three ligands together with the protein and pull the ligands one by one to calculate the binding energy. I am confused. Thanks in advance. Regards, Archana On Fri, Sep 28, 2012 at

Re: [gmx-users] Umbrella sampling-protein-ligand complex

On 9/28/12 9:27 AM, Archana Sonawani wrote: Hi, I have performed simulations for 3 different ligands complexed with the same protein. I want to compare the binding energies of these different three complexes. Will umbrella sampling be useful in this case? Several methods could be used, and

Re: [gmx-users] umbrella sampling (PMF) position discrepancy

Thank you all for your help, Sheeba- Yes, I get both positive and negative results. I think what you describe is what I would get if I used 'distance' for the geometry. In any case, I have values from +2 to about -3, and they are not evenly distributed (unlike the coordinates, which are more or le

Re: [gmx-users] umbrella sampling (PMF) position discrepancy

On 9/10/12 9:30 PM, Jianguo Li wrote: I guess is that g_wham takes the distance from tpr file which calculates the distance using grommp. It seems that the distances calculated using g_dist and grompp are different, as discussed in this forum about 10 days ago. This is a fairly frequent c

Re: [gmx-users] umbrella sampling (PMF) position discrepancy

: Discussion list for GROMACS users Cc: Sent: Monday, 10 September 2012, 23:54 Subject: Re: [gmx-users] umbrella sampling (PMF) position discrepancy Hi Justin, thank you for you quick reply. On Mon, Sep 10, 2012 at 6:41 PM, Justin Lemkul wrote: > > > On 9/10/12 11:22 AM, Raphael Alhad

Re: [gmx-users] umbrella sampling (PMF) position discrepancy

Hi Justin, thank you for you quick reply. On Mon, Sep 10, 2012 at 6:41 PM, Justin Lemkul wrote: > > > On 9/10/12 11:22 AM, Raphael Alhadeff wrote: > >> Dear Gromacs users, >> >> I've been trying to run an umbrella sampling (for the purpose of pmf) >> using >> Gromacs 4.5.5. >> My system consists

Re: [gmx-users] umbrella sampling (PMF) position discrepancy

On 9/10/12 11:22 AM, Raphael Alhadeff wrote: Dear Gromacs users, I've been trying to run an umbrella sampling (for the purpose of pmf) using Gromacs 4.5.5. My system consists of a membrane protein transporter and a Na ion passing through it, from the water bulk on one side of the membrane to t

Re: [gmx-users] Umbrella Sampling Pull code Problem

On Fri, Aug 31, 2012 at 1:45 PM, Steinbrecher, Thomas (IPC) wrote: > However, when I make the following two changes in my input file: > > pull_start = no > pull_init1 = 1.95 > > which should (?) amount to an equivalent setup, a very different trajectory > results in which the COM distan

Re: [gmx-users] Umbrella Sampling Pull code Problem

I have met similar problem before. The distance calculated by g_dist is different from that calculated by grommp, especially when the actual distance between the two groups is very small. As the actual distance becomes larger, the difference of the distance from the two commands becomes smalle

Re: [gmx-users] Umbrella sampling

On 8/10/12 1:14 PM, Paula Andrea Delgado Pinzon wrote: Good morning, I am trying to run an umbrella sampling simulation, my system is a complex of two proteins. I have a couple of questions: 1. i don't know which is the purpose in defining the charge of each protein end A net charge is a c

Re: [gmx-users] umbrella sampling

On 7/16/12 10:25 AM, Giovani Mancini wrote: Dear Gromacs users, I just read the tutorial by Justin Lemkul about umbrella sampling simulations along z-axis. My question is whether we need cylindrical confinement of the molecule that is pulling away from a reference molecule. Thanks in advance

Re: [gmx-users] umbrella sampling with distances larger than half box size

I would wait for others to answere but, a) you might try orienting your circular DNA in a visual program first and then use say just pull nny or something just as it makes it easier to see output and makes restraints nicer in output, b) the pull k1 might be larger for an effect on macromolecule

RE: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

Hello, I assume that you mean pull_pbcatom0... Nothing changes when I set this to an atom index I am afraid. I saw that you had use pull_geometry=cylinder in your recent JACS paper. Would it be too much to ask to see those pull settings? I simply cannot get the molecule to stay at the desired z-po

Re: [gmx-users] Umbrella Sampling Hypericin Dimer

On 4/30/12 12:26 PM, Hovakim Grabski wrote: Dear Gromacs users, I want to set up an umbrella sampling simulation of an Hypericin dimer. I have created position restraint filesfor hypericin with genrestr and then use it with the topology file, so I want to know if it is just restraining one of

Re: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

Hi, we had similar trouble some time ago, and we could solve it by using a good PBC atom. Make sure that your pbc_atom is in the very center of your membrane. Btw, using "distance" to compare with "cylinder" is a bad test, since it does something very different (the distance is the same at z

RE: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

> Does the cylinder geometry work if you use "pull_start = no" and pull_init1 > equal to your starting (restraint) distance? I'm just trying to go through > all > of the iterations of what might be failing. In theory, what you're doing is > fine but I'd be interested to know if there was som

Re: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

On 4/29/12 4:46 AM, J B wrote: > Is the problem specific to cylinder geometry? Do other settings work? Does it > make a difference if you set values for pull_r0 and pull_r1? > > -Justin I would think that it is the cylinder geometry that creates the problem. If I use pull = umbrella pull

RE: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

> Is the problem specific to cylinder geometry? Do other settings work? Does > it > make a difference if you set values for pull_r0 and pull_r1? > > -Justin I would think that it is the cylinder geometry that creates the problem. If I use pull= umbrellapull_geometry

Re: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

:31 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder > > > > On 4/28/12 5:12 AM, J B wrote: > > Hi. > > > > I am trying to the the PMF of tra

RE: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

Hi, the distance is 3.89 nm and the z-dimension is roughly 8 nm > Date: Sat, 28 Apr 2012 09:18:31 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Umbrella sampling PMF, drug and membrane with > pull_geometry=cylinder > > > &

Re: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

On 4/28/12 5:12 AM, J B wrote: Hi. I am trying to the the PMF of transferring a drug molecule from the aqueous phase to a lipid bilayer. In order to minimize the effects of membrane undulations I tried to use pull_geometry=cylinder. Whenever I run a short simulation with umbrella sampling st

Re: [gmx-users] Umbrella sampling along Radius of gyration

Hey Chris, It is actually not necessary to go to the code. You can do that by compiling a version of gromacs including the plumed path for free energy calculations. Amogst the several collective variables included there there is gyration radius. Regards Felipe Mensaje original---

Re: [gmx-users] Umbrella sampling multiple pull groups

Hi, somebody have an idea about this? Cheers Sabine On 03/09/2012 03:52 PM, Sabine Reisser wrote: Hi everyone, I'm trying to fold an unfolded peptide to a helix via umbrella sampling. I've defined 21 pulling groups, the C-Alpha atoms of the peptide, and i am restraining the distance between

Re: [gmx-users] Umbrella Sampling - Ligand Protein

Steven Neumann wrote: On Mon, Mar 12, 2012 at 11:06 AM, Justin A. Lemkul > wrote: Steven Neumann wrote: On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul mailto:jalem...@vt.edu> >> wrot

Re: [gmx-users] Umbrella Sampling - Ligand Protein

On Mon, Mar 12, 2012 at 11:06 AM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> >> >> On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Steven Neumann wrote: >> >>Hi Justin, >> As you advised I reduced number of my windows and

Re: [gmx-users] Umbrella Sampling - Ligand Protein

On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Hi Justin, >> As you advised I reduced number of my windows and I obtined histogram: >> http://speedy.sh/2b9dT/histo.**JPG >> Which looks really good. >> The correspond

Re: [gmx-users] Umbrella Sampling - Ligand Protein

Steven Neumann wrote: On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: Hi Justin, As you advised I reduced number of my windows and I obtined histogram: http://speedy.sh/2b9dT/histo.__JPG

Re: [gmx-users] Umbrella Sampling - Ligand Protein

Steven Neumann wrote: Hi Justin, As you advised I reduced number of my windows and I obtined histogram: http://speedy.sh/2b9dT/histo.JPG Which looks really good. The corresponding profile: http://speedy.sh/y8Ssz/profile.JPG I do not understand it. Does my deltaG of binding correspond

Re: [gmx-users] Umbrella Sampling - Ligand Protein

Hi Justin, As you advised I reduced number of my windows and I obtined histogram: http://speedy.sh/2b9dT/histo.JPG Which looks really good. The corresponding profile: http://speedy.sh/y8Ssz/profile.JPG I do not understand it. Does my deltaG of binding correspond to everything above 0 kcal/mol

Re: [gmx-users] Umbrella Sampling - Ligand Protein

On Thu, Mar 8, 2012 at 2:18 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Dear Gmx Users, Dear Justin, >> I pulled my ligand away from my protein. Ligand was attached to lower >> part of my protein, I pulled in Z coordinate it using: >> >> ; Run parameters >> >> integrator = md ;

Re: [gmx-users] Umbrella Sampling - Ligand Protein

Steven Neumann wrote: Dear Gmx Users, Dear Justin, I pulled my ligand away from my protein. Ligand was attached to lower part of my protein, I pulled in Z coordinate it using: ; Run parameters integrator = md ; leap-frog integrator nsteps = 500 ; 2 * 500 = 10 ns dt = 0.002 ; 2 f

Re: [gmx-users] Umbrella Sampling - NPT

Steven Neumann wrote: Dear Justin, I am wondering whether in NPT simulations before umbrella sampling in each window the option: continuation = yes should be set to continuation = no as you provided 1st option. The starting structures were the product of simulations that were previously

Re: [gmx-users] Umbrella sampling and WHAM along a curved pathway?

Hi, Jochen, Thanks a lot for your reply. I looked at the example header provided by g_wham -h. I just wonder if you can answer some more questions for me. The example header is # UMBRELLA 3.0 # Component selection: 0 0 1 # nSkip 1 # Ref. Group 'TestAtom' # Nr. of pull groups 2 # Group 1 'GR

Re: [gmx-users] Umbrella Sampling - gen_temp

Steven Neumann wrote: Dear Justin, Can I ask you why didnt you use in your mdp files for umbrella sampling (both MD and NPT): gen_temp = 310 ; temperature for Maxwell distribution I wasn't generating velocities in those steps, and as such, setting gen_temp was unnecessary. -Justin -

Re: [gmx-users] Umbrella Sampling - spacing

Thank you! On Wed, Feb 22, 2012 at 4:08 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Dear Gmx Users, Dear Justin, >> I run pulling of my ligand away from my protein. Then I used Justin perl >> script to extract distances for umbrella sampling windows between my ligand >> and cru

Re: [gmx-users] Umbrella Sampling - spacing

Steven Neumann wrote: Dear Gmx Users, Dear Justin, I run pulling of my ligand away from my protein. Then I used Justin perl script to extract distances for umbrella sampling windows between my ligand and crucial residue of my protein (Isoleucine). The number of hydrogen bonds between ligan

Re: [gmx-users] Umbrella sampling and WHAM along a curved pathway?

Hi, since there is no pull type for curved pathways, you have to generate the gmx3-type pdo files from your simlation output and use these in g_wham (g_wham -ip). See g_wham -h for a example header of a pdo file. Cheers, Jochen Am 2/14/12 5:53 PM, schrieb HAO JIANG: Dear all, I would lik

Re: [gmx-users] umbrella sampling tutorial quastion

As I know, it is not necessary to restrain neither reference nor pulled group. When you apply pulling force, it means you have restrained both of them. Dariush On Mon, Jan 9, 2012 at 4:15 PM, przemek bartha wrote: > Hello, > According to Justin's tutorial on umbrella sampling, > link: > http://w

Re: [gmx-users] umbrella sampling tutorial quastion

przemek bartha wrote: Hello, According to Justin's tutorial on umbrella sampling, link: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html could anyone explain, if the molecules are restrained in any way in the umbrella sampling part? The umbrel

Re: [gmx-users] Umbrella Sampling tutorial

Steven Neumann wrote: Hey Gmx Users, I went through Justin tutorial of umbrella sampling with spacing of 0.2 nm: Time COM distance 0 - 0.5 208 - 0.7 218 - 0.92 225 - 1.119 231 - 1.41 235 - 1.61 239 - 1.81 246 - 2.09 253 - 2.3 261 - 2.51 268 - 2.71 276 - 2.91 289 - 3.11 307 - 3.3 325

Re: [gmx-users] Umbrella Sampling - Justin tutorial

Thank you Justin! That helped a lot! Steven On Wed, Nov 16, 2011 at 3:06 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Thank you Justin, now I get what you mean! >> As I understood I should pick just one frame untill 189 ps (when >> dissociation occured) - does it matter which on

Re: [gmx-users] Umbrella Sampling - Justin tutorial

Steven Neumann wrote: Thank you Justin, now I get what you mean! As I understood I should pick just one frame untill 189 ps (when dissociation occured) - does it matter which one I will choose on the final binding free energy? The free energy minimum should (theoretically) be when the pepti

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