[gmx-users] Dissipative Particle Dynamics (DPD)

Dear all, since one of my mails with multiple questions went completely unanswered ( http://www.mail-archive.com/gmx-users@gromacs.org/msg15437.html ), let me try this time with more specific question. Is there any chance of Dissipative Particle Dynamics (DPD) being incorporated in Gromacs as a

[gmx-users] How to calculate scaling factors in the LIE equation

Dear all, I hope van der waals and electrostatic scaling factors in the LIE equation (g_lie) are system dependent (Ref: DK Jones-hertzog et al. 1996). Any one please give me a suggestion to calculate Clj and Cqq (as per g_lie program) in my protein-ligand system. I used GROMOS96 43a2 force field

Re: [gmx-users] QMMM

deAR       --- On Mon, 1/9/08, Pradip Biswas [EMAIL PROTECTED] wrote: From: Pradip Biswas [EMAIL PROTECTED] Subject: Re: [gmx-users] QMMM To: [EMAIL PROTECTED], Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, 1 September, 2008, 3:04 AM I believe it supports GAMESS UK,

Re: [gmx-users] QMMM

dear sir i am not aware of wheather interface is gamess UK or gamess US .but one thing if run configure -help command  in terminal, it shows the option  --with Gamess .sorry i am not able to reply correctely since i am beginner also in application side please sir be in touch .i am ver glad of

[gmx-users] Understanding of POPC analysis

Hi all, this may be trivial question to you. I am unfamiliar with gromacs. My doubt is that in POPC analysis most of the cases concerning about Z-axis why not X and Y. Can you please clear me this doubt. Thanks in advance for your suggestion.

[gmx-users] Changing LJ potential

Dear All, I need to define the LJ potential in a new way. Could anybody tell me where the LJ potential is calculated in the GROMACS files. -- Avinash Kumar. ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Understanding of POPC analysis

minnale wrote: Hi all, this may be trivial question to you. I am unfamiliar with gromacs. My doubt is that in POPC analysis most of the cases concerning about Z-axis why not X and Y. Can you please clear me this doubt. Thanks in advance for your suggestion. By convention, we think

[gmx-users] Using .pdb only

Hi There, I am usinng gromacs for running MDS of one protein, Can I use the pdb file only without generating the .gro file i.e. without using pdb2gmx ? If no, then how can I avoid addition of hydrogen during pdb2gmx ? With Thanks, Vivek ___ gmx-users

Re: [gmx-users] Using .pdb only

vivek sharma wrote: Hi There, I am usinng gromacs for running MDS of one protein, Can I use the pdb file only without generating the .gro file i.e. without using pdb2gmx ? Theoretically, yes. Gromacs can read a number of file formats at any stage (.pdb, .gro, etc). If no, then how can

[gmx-users] Bonds missing in VMD visualization

Hello, I have run an MD simulation of 1000 1,1,1-trichloroethane molecules and it all worked nicely. But when I try to visualize the trajectory file in VMD some of the C-Cl bonds are missing (although all the atoms appear on the screen - only bonds are missing)? Can I do anything to fix

Re: [gmx-users] Bonds missing in VMD visualization

VMD computes distances between pairs of atoms to draw a bond. So I think your atoms are too distanced from each other. Check the bond distribution during MD and compare with your topology. C-CL should be around 1.76A. VMD will not show this bond if, in the REFERENCE frame (the .gro/pdb you open

Re: [gmx-users] Re: g_velacc

Dear Vitaly Chaban, Thanks for your kind sugestions. I did followed the way you mentioned for calcualting the diffusion constants. I like to have a better understanding of what I have done. g_velacc: g_velacc -f -s -o -aceflen Since, mine is a single protein, I have not defined any index

Re[2]: [gmx-users] Re: g_velacc

Hi Ram, You should divide the value of your integral to the square of mass of you protein. Be attentive with units and powers then. I guess the final value will be essentially less than 0.99279 for floating protein. rr Here, though with the option -s we are calculting the momentum auto

[gmx-users] Re: g_velacc

Hi Ram, You should divide the value of your integral to the square of mass of you protein. Be attentive with units and powers then. I guess the final value will be essentially less than 0.99279 for floating protein. rr Here, though with the option -s we are calculting the momentum auto

Re: [gmx-users] Re: g_velacc

Hi Vitaly Chaban, The calcualted value of velocity autocorrelation function is 5.8*10^ -8 (momentum auto correlation function is 0.99279 and the protein mass is 4121.209 gm/mol). The resulting velocity auto correlation function will be in A^2/ps^2. If I devide this by a factor of 3, I will get

Re: [gmx-users] Re: g_velacc

rams rams wrote: Hi Vitaly Chaban, The calcualted value of velocity autocorrelation function is 5.8*10^ -8 (momentum auto correlation function is 0.99279 and the protein mass is 4121.209 gm/mol). The resulting velocity auto correlation function will be in A^2/ps^2. If I devide this by a

Fwd: Re[2]: [gmx-users] Re: g_velacc

rr Hi Vitaly Chaban, rr  rr The calcualted value of velocity autocorrelation function is 5.8*10^ -8 (momentum auto correlation function is 0.99279 and the protein mass is 4121.209 gm/mol). The resulting velocity auto correlation function will be in A^2/ps^2. If I devide this by a factor of 3, I

Re: [gmx-users] Re: g_velacc

Hi David Van der Spoel, You are right I missed the dt factor in the integral. Thanks a lot. Ram. On Mon, Sep 1, 2008 at 2:52 PM, David van der Spoel [EMAIL PROTECTED]wrote: rams rams wrote: Hi Vitaly Chaban, The calcualted value of velocity autocorrelation function is 5.8*10^ -8

[gmx-users] reg:merging of files

Dear users, I have a general question regarding the merging of files: 1. If suppose I am rerunning a job, the new tpr file is created in the following way: tpbconv -s .tpr1 -f .trr1 -o .tpr2 Here, no confusion. The run with new tpr2 would give me .trr2 file. Now if I want to rerun again,

Re: [gmx-users] reg:merging of files

rams rams wrote: Dear users, I have a general question regarding the merging of files: 1. If suppose I am rerunning a job, the new tpr file is created in the following way: tpbconv -s .tpr1 -f .trr1 -o .tpr2 Here, no confusion. The run with new tpr2 would give me .trr2 file. Now if I

[gmx-users] Bonds break while Minimising using distance restraints

Dear colleagues, I need to use simple distance restraints of 12.5 A between two CA atoms of two residues. I am using the following lines in the .itp file #ifdef DDISRES [distance_restraints] ;ai   aj type index type' low   up1  up2  fac 1703 1712 1    0 1    11.5  12.0 12.5 1.0 The first

Re: [gmx-users] Bonds break while Minimising using distance restraints

[EMAIL PROTECTED] wrote: Dear colleagues, I need to use simple distance restraints of 12.5 A between two CA atoms of two residues. I am using the following lines in the .itp file #ifdef DDISRES [distance_restraints] ;ai aj type index type' low up1 up2 fac 1703 1712 10 1

Re: [gmx-users] Dissipative Particle Dynamics (DPD)

there is dpdmacs available.. Regards, Yang Ye - Original Message From: Suman Chakrabarty [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, September 1, 2008 5:50:15 PM Subject: [gmx-users] Dissipative Particle Dynamics (DPD) Dear all, since

[gmx-users] Strange behavior from steepest descents

Hi all, I'm preparing a few membrane protein systems using the InflateGRO script from Tieleman's site. The bilayer consists of 340 POPE lipids, using structures and topologies from the same site. I've prepared several systems (with other lipids) using the methodology described, but am

[gmx-users] COM monitoring

Dear users, Is it possible to monitor the center of mass motion of a protein using gromacs tools since this is the one to monitor in most of the dynamical studies of the protein. Thanks in advance. Ram. ___ gmx-users mailing list

[gmx-users] Differences in version 3.0 and 3.3

Hi Chris, Thanks for your reply. I pretty much only changed the executable. The top/itp files did have to be modified a little bit because the formats were different, but all the parameters were the same. I basically wrote a script to convert the formats. Besides all the other energy

[gmx-users] How to calculate scaling factors in the LIE equation

Dear all, I hope van der waals and electrostatic scaling factors in the LIE equation (g_lie) are system dependent (Ref: DK Jones-hertzog et al. 1996). Any one please give me a suggestion to calculate Clj and Cqq (as per g_lie program) in my protein-ligand system. I used GROMOS96 43a2 force field

[gmx-users] Potential energy of POPC

Hi all, I have done popc simulation for 5ns and calculated potential energy of POPC. The values started from -269000 kj/mol reduced to -272000 kj/mol. Could you please tell me 1.is it require to extend my simulation from 5ns? 2. The above mentioned potential energy values whether correct

Re: [gmx-users] Dissipative Particle Dynamics (DPD)

Yang Ye wrote: there is dpdmacs available.. Yes, I know. But that seems to support only harmonic potential for even non-bonded interaction (DPD manual page 4-5), which is rather unphysical and not suitable for my purpose. Regards, Suman Chakrabarty.