[gmx-users] RMSF: Different results for same residue

for the same residues. Why is it so ?? Or am I making a mistake at some place ?? Thanks in advance. Alok -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before

[gmx-users] Diffusion by g_msd

molecules. my input command was g_msd -f XXX.xtc -s XXX.tpr -n index.ndx -o msd.xvg -type z -trestart 20 -b 5001 -e 5500 My question it is the correct way to calculate the diffusion for my desired water molecule within desired time? Regards, Alok -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Restraining molecular symmetry

correctly when prompted. But at least with some of the snap shots which I saw, I can find water mediated hydrogen bonds...Is there any other way to calculate solvent mediated hydrogen bonds.. Thanks in advance for your suggestions Alok -- This message has been scanned for viruses

Re: [gmx-users] angle and dihedral as a function of time

Try g_angle -h more specific g_angle -ov Alok - Original Message - From: SWAPNA [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, February 18, 2008 4:48 PM Subject: [gmx-users] angle and dihedral as a function of time Hi, Is there a way

Re: [gmx-users] Weird structure after minimization (membrane protein simulation)

flexible water molecules there is no such huge deviation from the original value.Also during the equilibration run I have not observed any LINCS warnings. I am hoping my problem is solved now :-) Thanks again to your valuable suggestions. Best regards, Alok Jain - Original Message

Re: [gmx-users] Weird structure after minimization (membrane proteinsimulation

and not in minimization. about comm_grps = Protein_POP SOL that was suggested by Dr. Xavier some time ago. http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ I will also try comm_grps = system and come back to you. Thanks again for your precious help. Regards, Alok - Original

[gmx-users] Weird structure after minimization (membrane protein simulation)

requesting expert comments from you people. Is it normal to Membrane simulation or there is some problem in my system? Till now I have not encountered any problems/warning. Eagerly waiting for your reply, Best regards, Alok Jain @Mark: Thanks a lot for your reply/comments and time. I am using TIP4P

Re: [gmx-users] [Fwd: Semiisotropic pressure coupling comm_grps (VCM)]

Dear Xavier, Thanks a lot for your reply. I will follow your suggestions. Best Regards, Alok - Original Message - From: Xavier Periole [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, November 26, 2007 5:23 PM Subject: Re: [gmx-users] [Fwd

[gmx-users] Semiisotropic pressure coupling comm_grps (VCM)

Dear All, I have two basic questions regarding membrane protein simulation. First regarding Semiisotropic pressure coupling (NPAT) and second regarding comm_grpp (VCM). 1) If I want to use NPAT ensemble (x/y dimensions of bilayer to be fixed) then is following the correct way to define?

Re: [gmx-users] make hole question

3.1.4 or previous - Original Message - From: Andrei Neamtu [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Saturday, November 17, 2007 11:29 PM Subject: [gmx-users] make hole question Hello gmx, I have a quick question: with what distribution of gromacs the mdrun make hole

[gmx-users] Removal of unwanted water from lipid bilayer after solvating the structure from genbox: problem and solution

suggestion), till now after 1ns run, my structure looks fine to me. Thanks a lot your and mark valuable suggestions and time. PS: If moderator permit me then I will post the picture (size 381 kb only) which will help to explain my problems and solution more clearly. Best Regards, Alok - Original

Re: [gmx-users] solvate using genbox results in water in the centerofthe bilayer. How to edit pdb file contents in gromacs ?

. Hope I will get any solution for my problem. Best Regards, Alok ## Dear Mark, Thanks a lot for your valuable time, and sorry for inappropriate description, I am describing again, I hope thin time I can make it clear. I took

Re: [gmx-users] solvate using genbox results in water in the centerofthe bilayer. How to edit pdb file contents in gromacs ?

Dear Chris, Thanks a lot your suggestions. I have started the MD based on your suggestions. I will tell you as soon I will get the results. PS: Is this is already reported that Gromacs have some problem with ZERO? Regards, Alok - Original Message - From: [EMAIL PROTECTED

Re: [gmx-users] alpha Carbon-Aromatic ring hydrogen bond

no) a ca1 (here ca1 is your CA hydrogen atom no) then you will get new index file containing these two groups. 2) Calculate the distance between these two groups using g_dist (as mark already suggested). Hope it will help. Alok - Original Message - From: sarbani chattopadhyay

Re: [gmx-users] solvate using genbox results in water in the center ofthe bilayer. How to edit pdb file contents in gromacs ?

it will help Alok - Original Message - From: maria goranovic To: gmx-users@gromacs.org Sent: Sunday, October 21, 2007 3:57 PM Subject: [gmx-users] solvate using genbox results in water in the center ofthe bilayer. How to edit pdb file contents in gromacs ? Hi I am using

Re: [gmx-users] uneven distribution of water across the bilayer

make my problem clear.could some one give some idea what parameters/ensemble I should take to overcome this problem. please suggest me where I am doing mistake. Thanks Regards, Alok - Original Message - From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx

[gmx-users] uneven distribution of water across the bilayer

Dear All, I am trying to simulate lipid-water system (340 POPE lipids 6120 TIP4P Waters), during the solvation by genbox, It also add the the water at the interior of the bilayer. I removed those water molecules by my perl script. But after removing these water molecules I have observed a

Re: [gmx-users] Restart

1.5ns Alok - Original Message - From: Mark Zottola To: Discussion list for GROMACS users Sent: Sunday, August 19, 2007 11:17 PM Subject: Re: [gmx-users] Restart Dil, Thanks for the post. However, my original job was set for 750 ps and ran successfully. Now, I would

Re: [gmx-users] 1-4 columb interaction

Thanks Chris for your detail reply. It really help me a lot. Regards, Alok - Original Message - From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Thursday, September 21, 2006 7:08 PM Subject: [gmx-users] 1-4 columb interaction Quoting Alok [EMAIL PROTECTED]: Thanks Chris

Re: [gmx-users] 1-4 columb interaction

, Alok - Original Message - From: Qiao Baofu To: Discussion list for GROMACS users Sent: Wednesday, September 20, 2006 7:17 PM Subject: Re: [gmx-users] 1-4 columb interaction In the force field file ff***.itp, there are two terms to scale lj and coloumb after

Re: [gmx-users] OPLS + ffgmx

to you later as I go about it. Thanking you all again, Regards, Alok. - Original Message - From: Mark Abraham [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, September 06, 2006 7:47 AM Subject: Re: [gmx-users] OPLS + ffgmx Hi all, I am

[gmx-users] OPLS + ffgmx

explicitly. Thanks a lot, Alok ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't

Re: [gmx-users] GROMACS with MPICH on Sun Cluster

able to run mdrun_mpi in the SUN CLUSTER) Warm regards, Alok Jain - Original Message - From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, June 08, 2006 11:11 PM Subject: Re: [gmx-users] GROMACS with MPICH on Sun Cluster

Re: [gmx-users] GROMACS with MPICH on Sun Cluster

Thanks again to your help. I will discuss these issues with my system administrator. I am really grateful for being a part of this excellent mailing list. Warm regards, Alok Jain - Original Message - From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx

[gmx-users] GROMACS with MPICH on Sun Cluster

# Any ideas regarding what is going wrong? Please let me know if you need more information... Thank you very much in advance, regards, Alok jain ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx