Re: [gmx-users] Rtp for polymer.

I connect the monomers by adding a bond in the rtp entry, in which the first atom of the next residue is given with + (you can also connect with the previous residue with - in front of the last atom). Sorry to explain this in a very confuse way. Better look at the example bellow (for polystyrene):

[gmx-users] Gromacs and ssh problem

Hi I installed Gromacs successfully on Fedora 8 nodes. Afterwards I ran a successful small simulation. Thereafter I moved the node to our server-room did the following: - set ip adress, subnetmask and gateway - changed the ssh port in /etc/ssh/sshd_config since we use port forwarding on our

RE: [gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator

Hi, I don't know why I did not add checks for ld-seed before. Now grompp gives a note when continutation=yes and ld-seed!=-1. tpbconv will now generate a new ld-seed when reading a trajectory (but you should not use tpbconv, use a checkpoint file instead). But yesterday I forgot to tell that

RE: [gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator

Hi, That I have thought about and it would avoid a lot of trouble. But I have not done that, because that would lead to different run results every time you rerun grompp, which can be misleading when you are trying to assess the effects of other parameters. But maybe the first issue is more

Re: [gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator

Hi, Maybe it's a good idea to have ld-seed=-1 as a default if that's not already the case. Ran. Berk Hess wrote: Hi, I don't know why I did not add checks for ld-seed before. Now grompp gives a note when continutation=yes and ld-seed!=-1. tpbconv will now generate a new ld-seed when reading

Re: [gmx-users] Gromacs and ssh problem

Bernhard Knapp wrote: Hi I installed Gromacs successfully on Fedora 8 nodes. Afterwards I ran a successful small simulation. Thereafter I moved the node to our server-room did the following: - set ip adress, subnetmask and gateway - changed the ssh port in /etc/ssh/sshd_config since we use

[gmx-users] heat exchanges

Dear Gromacs users, I am doing some tests with thermostats and I would like to know if someone has just done it. In particular: 1) How big has to be a protein to be coupled with a separate bath? 2) Do you know over which time scales a flux of heat is observed between protein and solvent

Re: [gmx-users] heat exchanges

On Feb 5, 2009, at 11:02 AM, Carlo Camilloni wrote: Dear Gromacs users, I am doing some tests with thermostats and I would like to know if someone has just done it. In particular: I have not done systematic tests but here are my impressions 1) How big has to be a protein to be coupled

Re: [gmx-users] heat exchanges

XAvier Periole wrote: On Feb 5, 2009, at 11:02 AM, Carlo Camilloni wrote: Dear Gromacs users, I am doing some tests with thermostats and I would like to know if someone has just done it. In particular: I have not done systematic tests but here are my impressions 1) How big has to be a

[gmx-users] Re: gmx-users Digest, Vol 58, Issue 31

available other than manual..If so please let me know Thanks in advance. -krithika -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090205/b73d8ab3/attachment-0001.html -- Message: 2

[gmx-users] Re: gmx-users Digest, Vol 58, Issue 33

Thank you, but is the conserved energy quantity written in the energy file compatible with the use of more than one temperature group? I ask this because in my tests seems that the conserved energy quantity is conserved better using only one temperature group. (I use pme for electrostatic and

Re: [gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator

Berk Hess wrote: Hi, That I have thought about and it would avoid a lot of trouble. But I have not done that, because that would lead to different run results every time you rerun grompp, which can be misleading when you are trying to assess the effects of other parameters. But maybe the

RE: [gmx-users] heat exchanges

Hi, Strictly speaking you should never have thermostats for separate parts of the system when those parts are coupled through potentials. But in practice you can have integration errors which heat or cool different parts of the system in different ways. I think that for most systems only the

[gmx-users] Re: IN4 molecule type error

Sorry for the mistake.. It worked well!!! Thank you... Aswathy Dept. Biotechnology Ext. 3108 - Original Message - From: gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org Sent: Tuesday, February 3, 2009 1:47:57 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: gmx-users

Re: [gmx-users] heat exchanges

Berk Hess wrote: Hi, Strictly speaking you should never have thermostats for separate parts of the system when those parts are coupled through potentials. But in practice you can have integration errors which heat or cool different parts of the system in different ways. I think that for most

[gmx-users] Is Gromacs CUDA compatible

Hello, Can anybody help me. I need to check if Gromacs is CUDA compatible. If not, is there any other middle-ware that will make it capable of GPU computing. Is CUDA compatibility in the pipeline for Gromacs. Any info would be greatly appreciable as I could not find any info on the web.

RE: [gmx-users] heat exchanges

From: x.peri...@rug.nl To: gmx-users@gromacs.org Subject: Re: [gmx-users] heat exchanges Date: Thu, 5 Feb 2009 15:24:28 +0100 On Feb 5, 2009, at 3:17 PM, David van der Spoel wrote: Berk Hess wrote: Hi, Strictly speaking you should never have thermostats for separate parts

Re: [gmx-users] heat exchanges

On Feb 5, 2009, at 3:17 PM, David van der Spoel wrote: Berk Hess wrote: Hi, Strictly speaking you should never have thermostats for separate parts of the system when those parts are coupled through potentials. But in practice you can have integration errors which heat or cool different

Re: [gmx-users] heat exchanges

On Feb 5, 2009, at 3:33 PM, Berk Hess wrote: From: x.peri...@rug.nl To: gmx-users@gromacs.org Subject: Re: [gmx-users] heat exchanges Date: Thu, 5 Feb 2009 15:24:28 +0100 On Feb 5, 2009, at 3:17 PM, David van der Spoel wrote: Berk Hess wrote: Hi, Strictly speaking you should

[gmx-users] heat exchanges

The integrations errors in the electrostatics have much more effect on the water than on the protein, because the water has higher charges and is far more mobile. No thermostat can correct for these errors, unless you use multiple groups. I realize that it is not exactly a thermostat, but the

RE: [gmx-users] heat exchanges

Date: Thu, 5 Feb 2009 10:27:13 -0500 From: chris.ne...@utoronto.ca To: gmx-users@gromacs.org Subject: [gmx-users] heat exchanges The integrations errors in the electrostatics have much more effect on the water than on the protein, because the water has higher charges and is far more

[gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator

My 24h tests on 200ps segments are also consistent with Berk's solution. SD runs with ld_seed=1993 results in a disaggregated micelle while ld_seed=-1 results in the same stability that I have seen previously using the MD integrator. This is not a surprise at this point, but I am posting the

[gmx-users] Residue name

Hello, I am trying to run a simulation using a surfactant and acetone molecules. I have residue name of ACT for my acetone molecule. When I perform energyminimization of my structure file, I end up having residue name of my surfactant all through the structure file. I have acetone.itp

[gmx-users] shake for water

All, A quick question on constraints... I'm using TIP4P-Ew in gromacs 3.3.2 and am concerned with reproducing energies from another code very precisely for several specific snapshots. I am doing a zero-step mdrun of a setup with one small molecule and two tip4p-ew water molecules. Anyway, I have

Re: [gmx-users] Residue name

Dinesh Pinisetty wrote: Hello, I am trying to run a simulation using a surfactant and acetone molecules. I have residue name of ACT for my acetone molecule. When I perform energyminimization of my structure file, I end up having residue name of my surfactant all through the structure

Re: [gmx-users] shake for water

David Mobley wrote: All, A quick question on constraints... I'm using TIP4P-Ew in gromacs 3.3.2 and am concerned with reproducing energies from another code very precisely for several specific snapshots. I am doing a zero-step mdrun of a setup with one small molecule and two tip4p-ew water

[gmx-users] heat exchanges

Thank you Berk, I have checked my temperature and find that there is no difference while using tau_t=0.1 or 1.0 (~2 ns): tau_t=0.1: temp=303.36 +/- 1.90 tau_t=1.0: temp=303.31 +/- 1.98 While using only one temperature coupling group, how would I ensure that the temperature of water is the

RE: [gmx-users] shake for water

Date: Thu, 5 Feb 2009 19:35:09 +0100 From: sp...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] shake for water David Mobley wrote: All, A quick question on constraints... I'm using TIP4P-Ew in gromacs 3.3.2 and am concerned with reproducing energies from

RE: [gmx-users] heat exchanges

Hi, With SD there are no temperature differences to be expected when the total temperature is correct. It could only go wrong in the very rare case that one group heats due to cut-off effects and another one cools due to inaccurate constraints. But because you get the same temperature at both

RE: [gmx-users] shake for water

Hi, Another question, just to be sure. Have you actually checked that the other code really gets the distances right up to 1e-12? Berk Date: Thu, 5 Feb 2009 12:03:21 -0600 From: dmob...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] shake for water All, A quick question on

Re: [gmx-users] shake for water

Berk Hess wrote: Date: Thu, 5 Feb 2009 19:35:09 +0100 From: sp...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] shake for water David Mobley wrote: All, A quick question on constraints... I'm using TIP4P-Ew in gromacs 3.3.2 and am concerned with

[gmx-users] about the repelling of DNA base pair

Hi all users, I am dealing with the CG DNA model and I just list the parameters for non-bond potential blow: A T 10.00690.04109 P P 10.04352 4.352E-12 S S 10.04352 4.352E-12 A A 1

Re: [gmx-users] Is Gromacs CUDA compatible

Hi, Just came across this page: https://simtk.org/project/xml/downloads.xml?group_id=161#package_id600 - you might want to check it out :) 2009/2/5 Jagdish S. Varma jsva...@connoiseur.com Hello, Can anybody help me. I need to check if Gromacs is CUDA compatible. If not, is there any other

RE: [gmx-users] shake for water

Hi, I don't agree. It uses the small 1+a approximation for the square. Also mdrun prints the rmsd determined with independent code, which is consistent with the (correct) tolerance. Berk Date: Thu, 5 Feb 2009 22:41:47 +0100 From: sp...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re:

RE: [gmx-users] shake for water

Hi David, I just checked with shake tolerance 1e-10 I really get deviations of 1e-10. First I forgot to turn on Shake and got the default Lincs, which with the default settings gave me roughly the accuracy you reported. (you did not by coincidence make the same mistake?) Berk From:

Re: [gmx-users] about the repelling of DNA base pair

He, Yang wrote: Hi all users, I am dealing with the CG DNA model and I just list the parameters for non-bond potential blow: People may care *which* CG model you are using... A T 10.00690.04109 P P 10.04352 4.352E-12 S

Re: [gmx-users] about the repelling of DNA base pair

He, Yang wrote: Hi all users, I am dealing with the CG DNA model and I just list the parameters for non-bond potential blow: A T 10.00690.04109 P P 10.04352 4.352E-12 S S 10.04352 4.352E-12 A

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Hey Mark, I am just not getting the theory behind doing position restraints and applying them to equilibrate. So let me frame my question well. Cu(I) is binding to three amino acids in the protein. Now If I remove Cu(I) the -1 charge of the protein changes to 0. So the protein has two specific

Re: [gmx-users] Free energy perturbation of Cu(I) binding

abhigna polavarapu wrote: Hey Mark, I am just not getting the theory behind doing position restraints and applying them to equilibrate. Sure... so that's why I recommended chapter 5 (which has an example of position restraints in section 5.7.1, which you can understand with references to

[gmx-users] Free energy perturbation of Cu(I) binding

You might benefit from reading Mobley, Chodera, and Dill. J. Chem. Theory. Comput. 2007, 3, 1231-1235. This paper doesn't relate exactly to your question, though, unless you do something like David initially suggested here

[gmx-users] g_hbond angle def

Hi list, What's the geometric relation b/w the commonly used Donor-H-Acceptor angle and the gromacs implementation of Acceptor-Donor-H angle? I guess I don't quite follow why it's valid to define the ADH cutoff as 30 degrees, the same angle most commonly used to define DHA, which suggests

[gmx-users] Reidue UNK not found

Hello I was using GROMACS 3.3.1 for few months and it was working pretty good. After that I wanted to use new GROMACS 4.0.3 but I came across a problem. I looked at GROMACS mailing list but I couldn't fix it. My code is: pdb2gmx -f nano.pdb -p nano.top and the error is:

RE: [gmx-users] Reidue UNK not found

May be of interest to you: http://wiki.gromacs.org/index.php/Carbon_Nanotube However, not surprising pdb2gmx failed, since UNK is not a residue specified in the residue database. pdb2gmx uses the residue name to determine what residue a particular part of your system is, then use the

Re: [gmx-users] g_hbond angle def

rob yang wrote: Hi list, What's the geometric relation b/w the commonly used Donor-H-Acceptor angle and the gromacs implementation of Acceptor-Donor-H angle? I guess I don't quite follow why it's valid to define the ADH cutoff as 30 degrees, the same angle most commonly used to define DHA,