Re: [gmx-users] Salt Bridge

Hi, I want to know the default cutoff distance g_saltbr tool uses in identifying the salt-bridges.. Regards -- Bharat -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] Hbonds per residue

Dear gromacs users, I have used g_hbond with -hbn option to generate a .ndx file. There is a method to plot the number of hbonds per residue in gromacs 4.5.5??? This issue is very confuse. Thanks for any suggestion!!! -- Natalia Alveal Fuentealba Ingeniera en Bioinformática Laboratory of

Re: [gmx-users] Interaction energy between helices

On 6/11/14, 5:36 PM, Natalia Alveal F. wrote: Dear Gromacs users, I want to calculate the energy of interaction between two helices of a protein, but g_energy dont have the option for -ndx file to select these specific residues of a helix. How I can do this? That's what energygrps in the

[gmx-users] how many groups shall I use to control the temperature?

Dear justin, I have doubts that whether I should use two groups to control the temperature or just one since there are just 604 hundred Protein beads and 6+ solvent beads. It is said that two groups are more accurate but when when i split them into two groups Protein nonProtein, I

Re: [gmx-users] Why does the list keep unsubscribing me?

This is the 4th time I am thrown out of the list by some random phishing email and I am done with this. If I am thrown out this time (I know I will be and no-one cares to fix any issues), I am not coming back. I just came back the last time to thank you folks for all your comments and helps

Re: [gmx-users] Why does the list keep unsubscribing me?

Hi, One simple solution is to subscribe with a different email address. Mark On Thu, Jun 12, 2014 at 9:54 AM, X Rules xru...@live.com wrote: This is the 4th time I am thrown out of the list by some random phishing email and I am done with this. If I am thrown out this time (I know I will

Re: [gmx-users] Hbonds per residue

Hi Natalia, It's a feature that has been requested a number of times, but has not been implemented yet unfortunately. Erik On 12 Jun 2014, at 00:50, Natalia Alveal F. nalv...@bio.puc.cl wrote: Dear gromacs users, I have used g_hbond with -hbn option to generate a .ndx file. There is a

[gmx-users] Energy minimisation step in Lipid protein simulation

Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as Ek! No confout.gro at all! Died at inflategro.pl line 104. What is confout.gro. If am right it is the output file that we get from the minimisation step. I used the command perl

[gmx-users] energy minimisation step in lipid protein simulation

Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as Ek! No confout.gro at all! Died at inflategro.pl line 104. What is confout.gro. If am right it is the output file that we get from the minimisation step. I used the command perl

[gmx-users] energy minimisation step in protein lipid simulation

Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as Ek! No confout.gro at all! Died at inflategro.pl line 104. What is confout.gro. If am right it is the output file that we get from the minimisation step. I used the command perl

[gmx-users] pH simulation

Hi everyone... I want to do pH simulation in gromacs . I didn't found any specific link that I can follow for calculation regarding pH . Can you please guide me ..Any link that can help me... Thanks in advance Regards Lovika -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] pH simulation

Hi, http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation Gromacs users list: http://comments.gmane.org/gmane.science.biology.gromacs.user/40950 https://www.mail-archive.com/gmx-users@gromacs.org/msg05430.html On Thu, Jun 12, 2014 at 2:44 PM, Lovika Moudgil

[gmx-users] energy minimisation in lipid protein simulation

Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as Ek! No confout.gro at all! Died at inflategro.pl line 104. What is confout.gro. If am right it is the output file that we get from the minimisation step. I used the command perl

[gmx-users] (no subject)

Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as Ek! No confout.gro at all! Died at inflategro.pl line 104. What is confout.gro. If am right it is the output file that we get from the minimisation step. I used the command perl

Re: [gmx-users] (no subject)

On 6/12/14, 5:31 AM, Balasubramanian Suriyanarayanan wrote: Why is my questions not appearing in the forum. Do I not follow the rules.' Please clarify. Your messages are being posted just fine. Please stop spamming the list. -Justin -- ==

Re: [gmx-users] Energy minimisation step in Lipid protein simulation

On 6/12/14, 4:54 AM, Balasubramanian Suriyanarayanan wrote: Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as Ek! No confout.gro at all! Died at inflategro.pl line 104. What is confout.gro. If am right it is the output file

Re: [gmx-users] how many groups shall I use to control the temperature?

On 6/12/14, 2:37 AM, 陈功 wrote: Dear justin, I have doubts that whether I should use two groups to control the temperature or just one since there are just 604 hundred Protein beads and 6+ solvent beads. It is said that two groups are more accurate but when when i split them into

Re: [gmx-users] -inf potential with TPIC

On 6/11/14, 8:55 PM, Rafael I. Silverman y de la Vega wrote: I mistyped amber, when I should have typed charmm, amber is totally uninvolved in my calculations. I used the script from http://www.gromacs.org/Downloads/User_contributions/Other_software titled charmm2gromacs. The output looked

Re: [gmx-users] (no subject)

i've recieved your email concernig energy minimisation step in protein lipid simulation already 3 times .. maybe you've deactivated the delivery of mails? if so, do the following: go to https://mailman-1.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users and log in where it says To unsubscribe

Re: [gmx-users] (no subject)

then, i don't know what to do. may be your email provider sorts them out or something. anyway, did you get justin's answer he sent recently? see below .. vedat On 6/12/14, 4:54 AM, Balasubramanian Suriyanarayanan wrote: Dear friends, In protein lipid simulation , when I do energy

Re: [gmx-users] (no subject)

i've recieved your email concernig energy minimisation step in protein lipid simulation already 3 times .. maybe you've deactivated the delivery of mails? if so, do the following: go to https://mailman-1.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users and log in where it says To unsubscribe

Re: [gmx-users] Tc grps, one group or two?

On Thu, Jun 12, 2014 at 4:11 AM, 陈功 gchen...@gmail.com wrote: Dear gromacs users, I have doubts that whether I should use two groups to control the temperature or just one since there are just 604 hundred Protein beads and 6+ solvent beads. It is said that two groups are more

Re: [gmx-users] Energy minimisation step in Lipid protein simulation

But is not confout.gro the output of the compression step. the command is perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat or else what is the output of above command. regards suriyanarayanan On Thu, Jun 12, 2014 at 3:13 PM, Justin Lemkul jalem...@vt.edu wrote: On

Re: [gmx-users] Why does the list keep unsubscribing me?

Thanks for the solution Mark, but from what I feel the right way to do is to fix mailman (add another option of clicking a link sent to your email to confirm unsubscribe, the same way subscription works). I might not be the only one, or may be I am the only one complaining :). Lets see how

Re: [gmx-users] Energy minimisation step in Lipid protein simulation

On 6/12/14, 7:14 AM, Balasubramanian Suriyanarayanan wrote: But is not confout.gro the output of the compression step. the command is perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat or else what is the output of above command. Read the InflateGRO documentation (top

Re: [gmx-users] Why does the list keep unsubscribing me?

Hi, I've no idea if mailman even has that option, or the KTH IT admins would be willing to set it up, but that's not worth exploring until automatic unsubscription is known to be a problem for more than one email address. Mark On Thu, Jun 12, 2014 at 1:34 PM, X Rules xru...@live.com wrote:

Re: [gmx-users] how many groups shall I use to control the temperature?

Thanks a lot, Justin. I do CG simulation using Martini force field. So maybe I can find some useful infomation on the forum of martini. Thanks :) From: Justin Lemkul Date: 2014-06-12 17:44 To: gmx-users Subject: Re: [gmx-users] how many groups shall I use to control the temperature? On

[gmx-users] Acpyte with opls-aa

Dear users i wanted to know if Acpyte generated topologies for a ligand are compatible with OPLS-AA.ff? i am searching for a reliable topology builder for OPLS-aa like ATP for gromos53a6.ff so that i can avoid manual approached like using  gaussian .  regards, Saman---BeginMessage--- Dear

Re: [gmx-users] g_clustsize

On 2014-06-12 15:33, Raisa Kociurzynski wrote: Dear Prof. Van der Spoel, I want to calculate the clustersize of GM1 clusters in a DPPC membrane. I used g_clustersize but when I use the option -mol the index file is ignored and the whole system is used for the calculation. Is there any way to

Re: [gmx-users] -inf potential with TPIC

Hello Rafael, High energies (energy differences) are not discarded. When summing them through the exponential of their negative, they contribute very little to the final sum (lower energies dominate the sum). Hence, they are discarded. The -inf value on the mu standard error output is normal

[gmx-users] question about topolbuild

Dear gmxusers, I have a question about using topolbuild to generate topology for my ligand (intend to use OPLS AA forcefield). However, I am facing a problem in using the command, which according to the README text, requires the basic input as below topolbuild -n modelname -dir

Re: [gmx-users] how many groups shall I use to control the temperature?

There is no rule regarding how many thermostats per system one needs. Often people choose separate thermostats for parts of system, which exhibit different mobility. I do not see any connection to functional forms of the interactions and, therefore, to force fields. Dr. Vitaly V. Chaban On

Re: [gmx-users] Interaction energy between helices

On 6/12/14, 2:02 PM, Natalia Alveal F. wrote: Thanks Justin, but for how long do this new simulation? It's not a new simulation. You're re-processing your existing trajectory. Usually the energy evaluations only take a few minutes. The practical impact of energygrps during a run is

[gmx-users] Adding residue at two end of DNA

Dear Gromacs User, Do you know how can I add some residue to ends of DNA? I am looking forward hearing of you,= Mahdi Bagherpoor -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] hardware problem of GPU?

thanks a lot. Finally both GPU are working. Albert On 06/11/2014 01:21 PM, Mark Abraham wrote: This is not a hardware issue. See http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Heterogenous_parallelization.3a_using_GPUs Mark -- Gromacs Users mailing list * Please

Re: [gmx-users] Using specbond.dat in pdb2gmx

On 6/11/14, 2:33 PM, Matthew Stancea wrote: ? Hello, I have been having a bit of issues generating an accurate gromacs topology file (topol.top) utilizing a pdb of a cyclic peptide in pdb2gmx. I have been able to generate topologies that are almost identical to the original pdb using the

Re: [gmx-users] Using specbond.dat in pdb2gmx

On 6/12/14, 4:53 PM, Matthew Stancea wrote: On 6/11/14, 2:33 PM, Matthew Stancea wrote: ? Hello, I have been having a bit of issues generating an accurate gromacs topology file (topol.top) utilizing a pdb of a cyclic peptide in pdb2gmx. I have been able to generate topologies that are almost

[gmx-users] about thermal intergation calculations

Hi All: I am trying to do free energy calculations by thermal integration method and I have read the tutorials on the gromacs web site, they are really nice tutorials and help me a lot. But I still have two questions here: 1, After we define the necessary paramteres in the mdp file (such as

Re: [gmx-users] Why does the list keep unsubscribing me?

Hi Mark, Thanks for your email. Firstly we don't even know if the exact problem is. It is just an assumption that this is happening. I understand that maybe I am the only one (or maybe others never got reported). Its just my attitude to try to remove bugs when I find and not wait for enough