Re: [gmx-users] problem in umbrella sampling

On 8/10/15 7:12 AM, Rajneet Kaur wrote: Hello sir, Thank you so much for response. I am beginner of gromacs. I don't understand how to make summery_distance.dat and group. Text and what is significance of these files in umbrella sampling groups.txt is made in a text editor. Its function

[gmx-users] Distribution of the TFE/Water molecules around a peptide

Dear users, My system is a peptide surrounded by TFE and water molecules. Since bibliography I can expect a preferential aggregation of TFE molecules around the peptide, after a 20 ns simulation and using VMD this effect is not obvious, but of course, I should analize more, for example the

Re: [gmx-users] Umbrella sampling sanity check

On 8/10/15 2:27 AM, Nash, Anthony wrote: Hi all, I would appreciate a little sanity check for umbrella sampling pull code parameters. My reaction coordinate is defined as the distance between a globular soluble enzyme and a substrate in solution (water). I have already captured the

Re: [gmx-users] Blowing up

On 8/10/15 1:42 PM, faride badalkhani wrote: Dear Victor, Thanks a lot for your answer. Could you introduce me a guidance for defining proper charge groups? The error message provides guidelines on what to do. With the Verlet scheme, charge groups are ignored. Without a better

Re: [gmx-users] Blowing up

Dear Victor, Thanks a lot for your answer. Could you introduce me a guidance for defining proper charge groups? Truly yours, Farideh On Mon, Aug 10, 2015 at 5:44 PM, Victor Rosas Garcia rosas.vic...@gmail.com wrote: it could be, but it might just be easier to try redefining smaller charge

Re: [gmx-users] Gromos 53a6, .mdp parameters for reaction field

As an update, After reading the suggested links I tried two .mdp files which were suggested in discussions as solutions. Both worked without any problem on my system. 1) rlist/r(columb/vdw)=(1.4/1.4) , in fact the problem seems to be the twin-range + RF 2) I used twin-range + RF BUT I reduced

Re: [gmx-users] Preparation of simulation system for GdmCl and protein simulation.

Hi all, Thank you very much for your reply Mark, Still if i see little variation of few molecules here and there as explained in my original post, should I go ahead with it ? I am requesting again, can someone please tell me which method people usually follow? On Sun, Aug 9, 2015 at 11:04 PM,

Re: [gmx-users] How to perform MD in TFE+solvent solution in Gromacs

Dear Dr. Justin, Thank you very much for your kind reply. ​-Bikash​ On Sat, Aug 8, 2015 at 8:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/8/15 3:00 AM, Bikash Ranjan Sahoo wrote: Dear all, I want to do MD simulation of my protein using simple water and water+TFE solvent. I have

[gmx-users] MD simulation using TFE

Dear All, I want to simulate my protein in 85 and 15 % water and TFE, respectively. Kindly guide me how to setup this system for a successful MD run. I have used the following commands. pdb2gmx_d -f test.pdb -o 1st.pdb -water spc -ignh -missing editconf_d -f 1st.pdb -o 2nd.pdb -bt cubic -c

Re: [gmx-users] Gromos 53a6, .mdp parameters for reaction field

Hi Mohsen, I am struggling with the same problem would you mind if I ask you to send me your .mdp file ? Cheers James On Tue, Aug 11, 2015 at 4:00 AM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: As an update, After reading the suggested links I tried two .mdp files which were

Re: [gmx-users] None constraints and l-bfgs.

Well, the *itp file says: #ifdef FLEXIBLE and there is bunch of lines defining proper parameters, so I assumed this is it. 2015-08-10 6:26 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: You've *tried* to use flexible water. But does your water itp file *have* a flexible implementation that

Re: [gmx-users] None constraints and l-bfgs.

Hi, OK, that sounds good. I ran your speedyshare files just fine with 4.6.7, so I think you are not using the files you think you are using. Mark On Mon, Aug 10, 2015 at 10:30 AM Dawid das add...@googlemail.com wrote: Well, the *itp file says: #ifdef FLEXIBLE and there is bunch of lines

Re: [gmx-users] None constraints and l-bfgs.

Hi, O'right, I will take a closer look. Thank you! 2015-08-10 10:11 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: Hi, OK, that sounds good. I ran your speedyshare files just fine with 4.6.7, so I think you are not using the files you think you are using. Mark On Mon, Aug 10, 2015 at

[gmx-users] Umbrella sampling sanity check

Hi all, I would appreciate a little sanity check for umbrella sampling pull code parameters. My reaction coordinate is defined as the distance between a globular soluble enzyme and a substrate in solution (water). I have already captured the individual windows using the trajectory generated from

Re: [gmx-users] Blowing up

it could be, but it might just be easier to try redefining smaller charge groups and run the dynamics again. Hope this helps Victor 2015-08-09 2:16 GMT-05:00 faride badalkhani farideh.kham...@gmail.com: Dear all, I am truing to do an MD simulation on dendrimeric structures. I can perform

[gmx-users] Position restraint some molecules of a moleculetype in a system

Hi all, I am using gromacs to run md simulation and I in my system I have 10 molecules of moleculetype A. I want to set position restraint for 3 molecules of moleculetype A and let 7 remained molecules relax. Can anyone help me to archive this goal? Thank you very much, Khuong -- Gromacs Users

Re: [gmx-users] Position restraint some molecules of a moleculetype in a system

Hi, Because [position_restraints] are a per-moleculetype directive, the only way you can do this is to have two [moleculetypes] and adapt your [molecules] section accordingly, so that the coordinate order still matches your topology order, e.g. [molecules] protein 1 ligand_a 2 ligand_a_restrained

[gmx-users] Warning with ewald-geometry = 3dc

Dear Gromcas Users, I am trying to run membrane protein simulation with slab geometry and EW3DC method (ewald-geometry = 3dc). As mentioned in the article http://www.cell.com/biophysj/abstract/S0006-3495%2803%2974458-0?mobileUi=0 , I have set up my system with extended Z-dimension and used pbc =