Category Archives: Tru-Dogan

Still Alive

It is hard not to keep laughing at the recent events in both Turkey and USA. Not because it is funny, but simply because there is nothing left to do besides laughing hysterically. I hope that there will be some countries left on the face of the earth in the upcoming years. Sure as hell, Turkey as in my imagination will not be there. It is already gone.

Trying to cheer up but geez it is tough. I still don’t like this city but I’ll be around for a little more for sure (being another year or two). I have come back from shopping and wondered once again why I am just not paying over 120$/week to Blue Apron & Hello Fresh to avoid it completely. Even ignoring doesn’t help in this city. I really don’t understand how things got this bad in this city. It is not the poverty I am talking about. To give an example, there is a culture of peeing in the streets. No! Not only the homeless does that. It is difficult to see what this city has to offer when I just feel fear walking down the street. Sure, Istanbul wasn’t superb, but I am not living there am I?

At least research is progressing. It is a slow progress, but I have completed the parametrization of my first molecule. Confession; I am close to be finished Getting used to analysis in charmm, learning to work with SAXS data, … and many more things. Some analyses are just too slow in CHARMM, like counting waters. But other things are nice. Being able to select the residues on the fly and not dealing with an index file for example is heaven. Parametrization is easier… I repeat easier.

I should find the time to update the toolbox and put up proper references to the scripts. Quite a few of them are based on Samuel Murail’s scripts I have inherited. Now I am inheriting quite many scripts from Justin Lemkul. Aa, I don’t think I have mentioned that I had work with him for a short while before he moved on to Virginia Tech. If you have used GROMACS, then you have definitely heard of him. It is safe to say he is one of the celebrities in the field 🙂 Rumor has it he is looking for postdocs if you are interested.

October… It is that time of the year again. Nobel Prize announcements, BPS abstract deadlines and my birthday. Unfortunately, this year too I won’t get to celebrate it. However, this year’s gift to me is the trip to San Francisco, and the BPS conference. I will submit my thesis cover painting to the image contest. When I dream too much about something, it doesn’t come true. Nevertheless, I shall see if I at least make it to the finals.


I cannot find any other words to describe the current political situations. Haha! One good thing that came out of Trump’s election as president… We are not alone anymore! I can’t stop giggling at what he said; can you believe it? Sweden!  The situation is no different from you-know-who saying one thing and the crowd cheering for the total opposite. I hope those crazy beings will leave us a world worth saving.

Life in Baltimore is getting better. Making progress in using Charmm, though I am not learning as fast as I would like it to be. But dealing with three countries is just too much. Taking care of taxes in Sweden, changing my address in Turkey so I can vote, filling in papers in USA… still filling in papers…

Some things just don’t make sense in this country. I know I have prejudice against the “system” here. Instead of seeing things as different, I see them as wrong. Paper sizes, how the apartment doors opens or not opens (you have to hold them), how they can deduct almost everything from my salary yet they ask me to write a check for the healthcare… I just don’t understand…

Oh I should mention that Baltimore is as expensive as Stockholm I would say. Give it a few more years and I bet it will be more expensive. There are definitely cheaper ways to live here, which is something almost didn’t exist in Stockholm. But I found those ways scary. Maybe because I think I cannot protect myself or maybe it is again the prejudice and looking down on people. I am seeing a new side of me. I just have to understand the roots of it so I can change it for the better.

Ah it could also be due to an empty house. While I get more and more things, I should, no, I will become happier. Lack of stuff certainly increases creativity; like I know now how to open a beer with a tiny screwdriver (it just takes time since I don’t have strength) or how to open a can with a knife and hammer…

Time… I just need to give myself and this city more time…