[gmx-users] how to neutralise: Non-integer charges

Dear users If you get a non-integer value for a charge, then how can you add charegs to your system? Eg: NOTE: System has non-zero total charge: -9.98e+00 This error is possibly due to the topology file but then how can it be recorrected? Thanks SIncerely Namitha

Re: [gmx-users] how to neutralise: Non-integer charges

On May 15, 2008, at 8:47, [EMAIL PROTECTED] wrote: Dear users If you get a non-integer value for a charge, then how can you add charegs to your system? Eg: NOTE: System has non-zero total charge: -9.98e+00 It's most probably due to rounding errors. Try to add ions worth 10 positive

Re: [gmx-users] how to neutralise: Non-integer charges

[EMAIL PROTECTED] skrev: Dear users If you get a non-integer value for a charge, then how can you add charegs to your system? Eg: NOTE: System has non-zero total charge: -9.98e+00 This error is possibly due to the topology file but then how can it be recorrected? Thanks SIncerely Namith

Re: [gmx-users] tip3p.gro

On 15 May 2008 10:28:13 - "sarbani chattopadhyay" <[EMAIL PROTECTED]> wrote: Hi, I am trying to run gromacs using charmm using the tip3p water model. I need the tip3p.gro file for this. Is there any way to get it? I have a '.itp' file specificaly for tip3p with charmm but not for tip4

Re: [gmx-users] atomname -> atomic number

> Mark Abraham wrote: >> Daniel Baum wrote: >>> Hi, >>> >>> I would like to write a reader for *.gro files, but I couldn't find any >>> information about how to map the atomname to the atomic number. Can >>> anyone shed some light on this problem? I would be most grateful. >> >> It's an ill-defined

[gmx-users] tip3p.gro

  Hi, I am trying to run gromacs using charmm using the tip3p water model. I need the tip3p.gro file for this. Is there any way to get it? I have a '.itp' file specificaly for tip3p with charmm but not for tip4p, though tip4p.gro is available . is there any way in which I can use the tip4

Re: Re: [gmx-users] tip3p.gro

 hi, that means i need to equlibrate the spc216.gro . Is there any specific temperature at which it needs to be done? I should continue with the equlibrated spc216.gro and this will yield the same result as tip3p? thanks in advance On Thu, 15 May 2008 Xavier Periole wrote : >On 15 Ma

Re: [gmx-users] tip3p.gro

On 15 May 2008 11:08:49 - "sarbani chattopadhyay" <[EMAIL PROTECTED]> wrote: hi, that means i need to equilibrate the spc216.gro . Is there any specific temperature at which it needs to be done? Depends what temperature you'll run later but I guess 300 K would be good. I should conti

[gmx-users] Re: Pressure and All-bonds

Problem resolved. All-Angles result in over-constrain if the number bonds+angles potentials are more than the number of constraints needed to keep molecule rigid. System configuration becomes semi-freezed - large clusters and a lot of empty space. Using any thermostat it gives the "correct" te

[gmx-users] (no subject)

Hi all, I ran protein simulation in water for 9ns and plotted RMSD but it didnt stabilize, iam doubting on steps what I have done I am mentioning the steps 1.EM in vaccum 2.PR in vaccum in NVT 3.EM in water 4.PR in water in NVT 5.Production run for 250 ps in NPT remain 9ns run in MVT condit

Re: [gmx-users] (no subject)

What you've done looks reasonable. Depending on how unstable the RMSD is, you may just have to simulate longer. Always remember to use a pertinent subject line when sending messages. That way more people are likely to respond if they see something of interest! -Justin Quoting minnale <[EMAIL

Re: Re: [gmx-users] RMSD plot

Quoting minnale <[EMAIL PROTECTED]>: > > Thanks for your prompt reply Justin > I am simulating 1ns each time, Due to this its happening? why i got this > doubt because at each 1ns, graph is showing either lowside fluctuations or > upside fluctuations. I don't understand what you mean. I doubt th

Re: [gmx-users] RMSD plot

Hi, On Thursday, 15. May 2008 18:04, Justin A. Lemkul wrote: > Quoting minnale <[EMAIL PROTECTED]>: > > Thanks for your prompt reply Justin > > I am simulating 1ns each time, Due to this its happening? why i got this > > doubt because at each 1ns, graph is showing either lowside fluctuations > > o

[gmx-users] RMSD plot

If I use the command in this way with option -mir insted of -o g_rms -f 9ns.xtc -n r20-50.ndx -mir mirror.xvg -pbc -s min.gro selected r_20-50 for least square fit group selected c-alpha for RMSD calculation if I plot a graph by using mirror.xvg file there is no fluctuations after

Re: [gmx-users] RMSD plot

minnale wrote: If I use the command in this way with option -mir insted of -o g_rms -f 9ns.xtc -n r20-50.ndx -mir mirror.xvg -pbc -s min.gro selected r_20-50 for least square fit group selected c-alpha for RMSD calculation if I plot a graph by using mirror.xvg file there is no fluc