[gmx-users] Replacing the PRODRG charges

I want to run a MD in an unparameterized molecule similar to adenine. I can get the approximated parameters in PRODRG. But I have read that PRODRG not always give the correct charge. Is it a good idea to replace that charges using the charges given with the R.E.D.vIII using ESP-A1 (suitable for

Re: [gmx-users] Replacing the PRODRG charges

Lucio Ricardo Montero Valenzuela wrote: I want to run a MD in an unparameterized molecule similar to adenine. I can get the approximated parameters in PRODRG. But I have read that PRODRG not always give the correct charge. Is it a good idea to replace that charges using the charges given with

[gmx-users] how to include ionic strength

Dear gromacs users,   I am simulating a protein which works in salt solution within cell. I have to include 4M salt (say, NaCl) to the simulation box. How can i include such ionic strength? Please outline me the procedure.   Thanks in advance. Amrita Paul     Cricket on your mind? Visit

Re: [gmx-users] how to include ionic strength

amri ta wrote: Dear gromacs users, I am simulating a protein which works in salt solution within cell. I have to include 4M salt (say, NaCl) to the simulation box. How can i include such ionic strength? Please outline me the procedure. If you do some tutorial material, you will find out

[gmx-users] DSSP problem

Dear all I want ti install DSSP for visualization of secondary structure in gromacs analysis. I am doing following procedure.. Copy the executable dsspcmbi to /usr/bin or /usr/local/bin ln -s dsspcmbi dssp And running it for my Pdb like that dssp file.pdb file.dssp BUt I am getting error

Re: [gmx-users] DSSP problem

rituraj purohit wrote: Dear all I want ti install DSSP for visualization of secondary structure in gromacs analysis. I am doing following procedure.. Copy the executable dsspcmbi to /usr/bin or /usr/local/bin ln -s dsspcmbi dssp And running it for my Pdb like that dssp file.pdb file.dssp

[gmx-users] DSSP problem

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[gmx-users] gromos type in .rtp file

hello everyone Can any body please explain to me, what does the trm gb_38 or gb_39 stand for under the bond coulmn of the .rtp file ? what is gromos type under angles and impropers? Subarna Explore and discover exciting holidays and getaways with Yahoo! India Travel

Re: [gmx-users] gromos type in .rtp file

On Jun 4, 2009, at 10:10 AM, subarna thakur wrote: hello everyone Can any body please explain to me, what does the trm gb_38 or gb_39 stand for under the bond coulmn of the ..rtp file ? what is gromos type under angles and impropers? gb_XX stands for the XX type of gromos bond, ga_XX for

Re: [gmx-users] DSSP problem

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[gmx-users] gromacs website: (There is currently no text in this page)

Hi, there seems to be a discrepancy between google results from the gromacs pages and the pages themselves. If going to results on the mailing list or for example: www.*gromacs*.org/documentation/howtos/*mpich*_howto.html I see the gromacs page, and the submenu seems to be ok, but the page is

Re: [gmx-users] gromacs website: (There is currently no text in this page)

pim schravendijk wrote: Hi, there seems to be a discrepancy between google results from the gromacs pages and the pages themselves. If going to results on the mailing list or for example: www.*gromacs*.org/documentation/howtos/*mpich*_howto.html I see the gromacs page, and the submenu

Re: [gmx-users] gromacs website: (There is currently no text in this page)

Ah yes, but can't you configure an automatic server forward to do this? I can't imagine many people want to manually retype the url they get as a google result. On Thu, Jun 4, 2009 at 2:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: pim schravendijk wrote: Hi, there seems to be a

Re: [gmx-users] DSSP problem

rituraj purohit wrote: Dear mark Where i can get the file with permission. I downloaded from http://swift.cmbi.kun.nl/gv/dssp/ Please do not send copies of entire digests in your emails. That breaks searches and wastes time and bandwidth. You give the file permissions in the standard Unix

Re: [gmx-users] Replacing the PRODRG charges

The target forcefield will be G43a1. But I would move to more recent versions of GROMOS 53a5 or 53a6. El jue, 04-06-2009 a las 16:29 +1000, Mark Abraham escribió: Lucio Ricardo Montero Valenzuela wrote: I want to run a MD in an unparameterized molecule similar to adenine. I can get the

[gmx-users] Scaled 1-5 interactions

Dear GROMACS Users, I would like to use the OPLS force field, but with additional scaling factor for the Coulomb 1-5 interactions for certain atoms. More precisely, I want to use the standard 0.5 scaling for Coulomb and LJ 1-4 interactions and 0.8 scaling factor for Coulomb 1-5 interactions. Is

[gmx-users] Entending water in negative Z direction

Hi ALL, In previous posts I mentioned the problem I am facing: a portion of my protein (GPCR in a POPC bilayer) in extending out of the water box in negative Z-direction, how to extend the water in that direction. I have gone through the PBC section of the manual. While changing the Z

Re: [gmx-users] Entending water in negative Z direction

Anirban Ghosh wrote: Hi ALL, In previous posts I mentioned the problem I am facing: a portion of my protein (GPCR in a POPC bilayer) in extending out of the water box in negative Z-direction, how to extend the water in that direction. I have gone through the PBC section of the manual. While

[gmx-users] diffusion coefficient with g_msd

Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate the diffusion coefficient of the molecules inside the membrane, and therefore I looked at g_msd. The manual (version 4.0) states on p. 250 (manual

[gmx-users] Entending water in negative Z direction

If you are using PBC, extending the positive direction *is* extending the negative direction, they are the same thing. If you really must center your bilayer on Z, then try editconf -translate 0 0 N And please take this only as a useful suggestion, but simulating a GPCR in a membrane

Re: [gmx-users] Replacing the PRODRG charges

Lucio Ricardo Montero Valenzuela wrote: The target forcefield will be G43a1. But I would move to more recent versions of GROMOS 53a5 or 53a6. A more empirical charge assignment is often a reasonable starting point for assigning GROMOS charges. As I understand it, quantum calculations were

Re: [gmx-users] gromacs website: (There is currently no text in this page)

pim schravendijk wrote: Ah yes, but can't you configure an automatic server forward to do this? I can't imagine many people want to manually retype the url they get as a google result. The transition period is presumably not going last very long, and I'd rather put up with some temporary

Re: [gmx-users] Entending water in negative Z direction

Hi, What is the difference between increasing in the positive z direction and the negative z direction? Tsjerk On Thu, Jun 4, 2009 at 4:31 PM, Anirban Ghosh anirban...@yahoo.co.in wrote: Hi ALL, In previous posts I mentioned the problem I am facing: a portion of my protein (GPCR in a POPC

Re: [gmx-users] Replacing the PRODRG charges

On Thu, Jun 04, 2009 at 03:46:59PM -0400, Justin A. Lemkul wrote: Lucio Ricardo Montero Valenzuela wrote: The target forcefield will be G43a1. But I would move to more recent versions of GROMOS 53a5 or 53a6. A more empirical charge assignment is often a reasonable starting point for

[gmx-users] overrriding problem

Hi, I am doing a simulation combining amber and Gaff force field (for dopc lipids), this is the first part of my topology file: ; UNK_GMX.top created by acpypi on Thu Jun 4 22:06:03 2009 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2

[gmx-users] Re: goverrriding problem

Yep, contrary to AMBER, GMX is not case sensitive, so C and c are the same and since you declare them twice you get this overriding warning. However, I did acpypi aware of this (it should add '_' to e.g. c, making 'c_'). Unless you're doing something manually (as it seems). Otherwise it would a

[gmx-users] g_hbond error

Hi, Has any one encountered this error while using g_hbond? * Select a group: 12 Selected 12: 'SOL' Select a group: 12 Selected 12: 'SOL' Calculating hydrogen bonds in SOL (20949 atoms)

Re: [gmx-users] g_hbond error

krishnakumar wrote: Hi, Has any one encountered this error while using g_hbond? * Select a group: 12 Selected 12: 'SOL' Select a group: 12 Selected 12: 'SOL' Calculating hydrogen bonds in SOL (20949 atoms)

RE: [gmx-users] Re: goverrriding problem

Thank you very much, Alan. In this case, I am not using acpypi, since I am using a topology for dopc already published, and it is already converted into Gromacs. So, it´s manually, as you suppose. I will follow your suggestion and change c and o by c_ and o_. Best wishes, Rebeca. From:

Re: [gmx-users] Scaled 1-5 interactions

Borys Szefczyk wrote: Dear GROMACS Users, I would like to use the OPLS force field, but with additional scaling factor for the Coulomb 1-5 interactions for certain atoms. More precisely, I want to use the standard 0.5 scaling for Coulomb and LJ 1-4 interactions and 0.8 scaling factor for

[gmx-users] reference group in constant velocity pulling, GMX 4

Dear all, I am using the pulling code in gromacs 4.0.5 with constant velocity pulling. My case is pulling protein in two opposite directions, which I do not want any other extra force acting on the protein. So I did not assign any reference group in the simulation, and I got a warning saying