Re: [gmx-users] what is cgnr ?

Chih-Ying Lin wrote: Hi In the .top file, [atoms] section, cgnr is given. Could any one explain more about the cgnr? cgnr = charge group number Read the relevant entries on charge groups for more information. -Justin Manual does not say it more. Thanks Lin

[gmx-users] what is cgnr ?

Hi In the .top file, [atoms] section, cgnr is given. Could any one explain more about the cgnr? Manual does not say it more. Thanks Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please se

[gmx-users] Re: minimize multi-chain protein

HI, I am using gromacs for energy minimization. Can anyone advise me on how to do this for a multi-chain protein. When I try to minimize a protein with multiple chains, gromacs creates a bond between the last residue of the previous chain and the first residue of the next chain, not recognizing

[gmx-users] g_wham.c

Hello, I've read the threads but could not find the file itself, or the needed corrections for the existing g_wham.c. Is anyone able to send me a copy of the corrected g_wham.c by David Bostick of Scripps. Thank you. __ Venkatesh Hariharan Pennsylvania State Un

Re: [gmx-users] Re: Question about Berendsen thermostat and

On Thu, 24 Jul 2008, David van der Spoel wrote: Michael Shirts wrote: Thanks for the tip! You're welcome! That thermostat is really nice and also simple to implement. It is now in CVS. If this thermostat has a stochastic term, is the dynamics still meaningful then? Of course it's not! N

Re: [gmx-users] Possible Bug????

Matthew Danielson wrote: Thanks for the reply, but i am a little unsure why the number of "atoms/coordinates" do not match. My eigenvec.trr has 1401 atoms (this was created using the same default index file to select the backbone) and it should match what is in my index file (or tpr). If i l

[gmx-users] Possible Bug????

What do you get from gmxcheck -f eigenvec.trr ?? If you still have more problems you may want to consider submitting under a title that is a) more descriptive, and b) makes an attempt to avoid the word bug. --original message-- Users, I am having a problem when trying to convert a .trr to a

Re: [gmx-users] Possible Bug????

Thanks for the reply, but i am a little unsure why the number of "atoms/coordinates" do not match. My eigenvec.trr has 1401 atoms (this was created using the same default index file to select the backbone) and it should match what is in my index file (or tpr). If i look at the index group lis

Re: [gmx-users] Possible Bug????

Matthew Danielson wrote: Users, I am having a problem when trying to convert a .trr to a .pdb using trjconv. I think there could there be a bug in the program and the index group is getting confused. Here is exactly what i am doing: Command: trjconv -f eigenvec.trr -s prot_md.gro -o tes

[gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling

Hi all, Very interesting discussion ! Here are a few thoughts on two points that appeared in the last digest: David: But does the NH chain, the mother of all thermostats, indeed yield correct dynamics? No it does not, if what you call correct dynamics is the Hamitlonian dynamics corre

[gmx-users] Possible Bug????

Users, I am having a problem when trying to convert a .trr to a .pdb using trjconv. I think there could there be a bug in the program and the index group is getting confused. Here is exactly what i am doing: Command: trjconv -f eigenvec.trr -s prot_md.gro -o test.pdb Output: Will write p

Re: [gmx-users] Re: gmx-users Digest, Vol 51, Issue 89

shahrbanoo karbalaee wrote: Dear justin Thank you again. but about if i use TFE for solvent instead of water ,how can apply dielectric constant in program and only I can TFE instead of spc/e.what about PH?and counter ion ? All of these questions can be answered by finding the appropriate ref

Re: [gmx-users] Re: Question about Berendsen thermostat and

> On that topic: There is a recent paper from the Tavan group where they > carefully discuss and investigate the effects of different > thermostats. They also come up with a "noninvasive" thermostatting > procedure where they couple a Berendsen thermostat to the solvent only > such that it acts as

RE: [gmx-users] box size changing during isotropic pressure coupling

Hi, The triclinic case shows a systematic looking difference between x/y and z. But here x and y are really identical, so they will always stay identical. The magnitude of the effect is very small though. I would not worry about it. I don't think it is worth putting more effort into, since it has

[gmx-users] Doubt regarding popc simulations

Unless your membrane is extraordinarily large, your cutoffs extraordinarily long, or your computational resources extraordinarily small, then I suggest that you simulate for 50ns and then analyze the convergence of these properties yourself. I have often posted the 50 ns suggestion to this list

[gmx-users] box size changing during isotropic pressure coupling

Here tau_p=4, which is already quite large. But there are no "real" problems in the system, the results should be fine. But the relative ling tau_p might be the reason for the strange scaling. This would make the scaling factor always close to 1 plus or minus one bit. I have not done the binary ma

RE: [gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling ([EMAIL PROTECTED])

Hi, Indeed, read the paper! The stochastic term works on the "Berendsen scaling parameter" only. It has the same correlation time as tau_t. So the dynamics is nearly unaffected, surely less than with Nose-Hoover. Berk. > Date: Thu, 24 Jul 2008 17:26:00 +0200 > From: [EMAIL PROTECTED] > To: gmx-

[gmx-users] box size changing during isotropic pressure coupling

Thanks for the assistance Berk, Hmm... this is a (seemingly( really systematic decrease in x and y and increase in z. But is x at the start really EXACTLY identical to y? No. Here are the starting dimensions: 19.58000 19.39000 21.04200 That is prior to 200ps run with position restraints

Re: [gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling ([EMAIL PROTECTED])

>> See: http://arxiv.org/abs/0803.4060. It might be nice to replace for those who havent already - download the paper - it contains a background with all the references you need for thermostats Andersons "landmark" paper in 1980 (as I gave) - Noses 1984 paper etc. David __

[gmx-users] Doubt regarding popc simulations

Hi all, I want to ask one question regarding time of POPC simulations, this may be trivial query to you that is how long time normally popc alone simulations have to run? I know that if potential energy plot shows values from high to low which depicts stable graph we can stop the simulation

Re: [gmx-users] Re: Question about Berendsen thermostat and

On 24 Jul 2008, at 16:57, David van der Spoel wrote: Michael Shirts wrote: Thanks for the tip! You're welcome! That thermostat is really nice and also simple to implement. It is now in CVS. If this thermostat has a stochastic term, is the dynamics still meaningful then? Of course it's not!

[gmx-users] Hydrogen Database Format - Control Atoms

Hello all, In the Gromacs Manual 3.3 the format for the hydrogen database is given in section 5.5.2. It follows that the format for each addition is: number of H atoms way of adding the H atom name of the H atom 3 or 4 control atoms In regards to the 3 or 4 control atoms the manual states: Thr

Re: [gmx-users] Re: Question about Berendsen thermostat and

Hi all On that topic: There is a recent paper from the Tavan group where they carefully discuss and investigate the effects of different thermostats. They also come up with a "noninvasive" thermostatting procedure where they couple a Berendsen thermostat to the solvent only such that it a

Re: [gmx-users] Re: Question about Berendsen thermostat and

Michael Shirts wrote: Thanks for the tip! You're welcome! That thermostat is really nice and also simple to implement. It is now in CVS. If this thermostat has a stochastic term, is the dynamics still meaningful then? Of course it's not! No thermostat gives physical dynamics. But at least

Re: [gmx-users] Re: Question about Berendsen thermostat and

>> Thanks for the tip! You're welcome! >> That thermostat is really nice and also simple to implement. >> It is now in CVS. > If this thermostat has a stochastic term, is the dynamics still > meaningful then? Of course it's not! No thermostat gives physical dynamics. But at least it gives the c

Re: [gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling ([EMAIL PROTECTED])

Berk Hess wrote: Hi, That thermostat is really nice and also simple to implement. It is now in CVS. If this thermostat has a stochastic term, is the dynamics still meaningful then? (I haven't read the paper of course :)). Thanks for the tip! Berk. > Date: Wed, 23 Jul 2008 10:12:36 -040

[gmx-users] Re: gmx-users Digest, Vol 51, Issue 89

Dear justin Thank you again. but about if i use TFE for solvent instead of water ,how can apply dielectric constant in program and only I can TFE instead of spc/e.what about PH?and counter ion ? best karbalaee ___ gmx-users mailing listgmx-users@grom

RE: [gmx-users] box size changing during isotropic pressure coupling

Hi, Here tau_p=4, which is already quite large. But there are no "real" problems in the system, the results should be fine. But the relative ling tau_p might be the reason for the strange scaling. This would make the scaling factor always close to 1 plus or minus one bit. I have not done the binar

RE: [gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover temp coupling ([EMAIL PROTECTED])

Hi, That thermostat is really nice and also simple to implement. It is now in CVS. Thanks for the tip! Berk. > Date: Wed, 23 Jul 2008 10:12:36 -0400 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] Re: Question about Berendsen thermostat and Nose-Hoover > temp cou

Re: [gmx-users] box size changing during isotropic pressure coupling

Berk Hess wrote: Hi, Hmm... this is a (seemingly( really systematic decrease in x and y and increase in z. But is x at the start really EXACTLY identical to y? Because in that case I would think they should always stay identical. But looking at the code I see that it is always uses triclinic

Re: Re: [gmx-users] doesn't match coordinate file with topology

Thank you Peyman On Thu, 24 Jul 2008 Peyman Yamin wrote : >On Thursday 24 July 2008 09:46, minnale wrote: > > Hi users, > > I have generated .gro file of protein by using .xtc file with trjconv > > command after that i used pdb2gmx command for generating topology file > > without any erro

Re: [gmx-users] doesn't match coordinate file with topology

On Thursday 24 July 2008 09:46, minnale wrote: > Hi users, > I have generated .gro file of protein by using .xtc file with trjconv > command after that i used pdb2gmx command for generating topology file > without any error. when I have inserted this protein into popc bilayer by > using genbox

RE: [gmx-users] box size changing during isotropic pressure coupling

Hi, Hmm... this is a (seemingly( really systematic decrease in x and y and increase in z. But is x at the start really EXACTLY identical to y? Because in that case I would think they should always stay identical. But looking at the code I see that it is always uses triclinic scaling. Thus x and

[gmx-users] doesn't match coordinate file with topology

Hi users, I have generated .gro file of protein by using .xtc file with trjconv command after that i used pdb2gmx command for generating topology file without any error. when I have inserted this protein into popc bilayer by using genbox command i has deleted some of the water and popc m